tag:blogger.com,1999:blog-17378048288529941042024-03-02T16:39:01.805+08:00Bioinformatics TutletsAsif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.comBlogger43125tag:blogger.com,1999:blog-1737804828852994104.post-10255586814669074442019-11-05T19:54:00.001+08:002019-11-05T19:59:19.850+08:0041) Running AVANA on a Mac / Linux machineAlthough the AVANA tool is build using Java, the installer available on SourceForge (https://sourceforge.net/projects/avana/) is custom-built for Windows machines. In order to run it on a Mac or Linux machine, one needs to follow the steps below:<br />
<br />
1) Download the tool executable from https://sourceforge.net/projects/avana/<br />
<br />
2) Install the file by double clicking on the downloaded file. While installing, if you don't have certain java run time environment file, you will be promoted to download. Complete the download and installation of the Java files. Then try installing again. During the installation process, you would be asked where to install Avana. It would be preferred to not install this in the Applications folder, instead save it in an easy to find directory under your user profile, such "/Users/asif/Downloads/AVANA", where "AVANA" is a folder you created under the "Downloads".<br />
<br />
3) Go to the folder where you installed AVANA. For this tutorial, let's say it is installed in "/Users/asif/Downloads/AVANA". Go to that folder and you should see a bunch of files, in particular a file entitled "runAvana.bat". We would need to either convert this Windows batch file (*.bat) to a Unix batch file (*.sh). To do this, either rename the windows batch file to "runAvana.sh" or create a new file with the name "runAvana.sh". You can choose to either keep or delete the "*.bat" file, it would not affect the execution of AVANA on a Mac / Linux machine.<br />
<br />
4) Open the "runAvana.sh" file and delete the existing content inside. Then paste the following new content to the file:<br />
<br />
#!/bin/bash<br />
<br />
export AVANA_HOME=/Users/asif/Downloads/AVANA<br />
export CLASSPATH=$AVANA_HOME/avana.jar:$AVANA_HOME/avana-gui.jar:$AVANA_HOME/lib/biojava-1.4.jar:$AVANA_HOME/lib/bytecode-0.92.jar:$AVANA_HOME/lib/commons-beanutils-1.7.0.jar:$AVANA_HOME/lib/commons-logging-1.1.jar:$AVANA_HOME/lib/commons-math-1.1.jar:$AVANA_HOME/lib/jcommon-1.0.0.jar:$AVANA_HOME/lib/jfreechart-1.0.1.jar<br />
<br />
java -Xms256m -Xmx800m it.southdown.avana.ui.AvanaGUI<br />
<br />
<br />
5) In your case, replace the path (/Users/asif/Downloads/AVANA) in "AVANA_HOME" line to where you have installed the tool.<br />
<br />
6) Open the Terminal. Navigate to the folder (/Users/asif/Downloads/AVANA) on the Terminal.<br />
<br />
7) Make the "runAvana.sh" file executable through the following command:<br />
<br />
chmod a+x runAvana.sh<br />
<br />
8) Execute Avana:<br />
<br />
sudo ./runAvana.sh<br />
<br />
9) Sudo is to give you admin access in case you need authorisation. Enter the administrator password of your computer when prompted.<br />
<br />
10) Done! Enjoy measuring entropy!<br />
<br />
<br />Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-7224757628518930992099-03-21T05:17:00.000+08:002019-11-05T19:55:24.641+08:00All Posts<div>
<div>
<div>
41) <a href="http://bioinfotutlets.blogspot.com/2019/11/41-running-avana-on-mac-linux-machine.html" target="_blank">Running AVANA on a Mac / Linux machine</a><br />
40) <a href="http://bioinfotutlets.blogspot.com/2010/08/include-database-id-into-blast-result.html">How to include my own database ID along with the NCBI ID on the BLAST's result page?</a></div>
<div>
39) <a href="http://bioinfotutlets.blogspot.com/2010/03/39-how-to-create-password-protected.html">How To Create a Password Protected Website</a></div>
<div>
38) <a href="http://bioinfotutlets.blogspot.com/2010/03/running-blast-cleint-on-mac-osx.html">Running Blast+ client on Mac OSX</a></div>
<div>
37) <a href="http://bioinfotutlets.blogspot.com/2009/12/37-making-blast-hits-into-fasta-format.html">LAPIS: Converting blast hit sequences into fasta format</a></div>
<div>
36) <a href="http://bioinfotutlets.blogspot.com/2009/09/openbabel-gui-file-format-converter.html">OpenBabel GUI - file format converter</a></div>
<div>
35) <a href="http://bioinfotutlets.blogspot.com/2009/09/autodock-40-installation-and-working.html">Autodock 4.0 (Installation and working)</a></div>
<div>
34) <a href="http://bioinfotutlets.blogspot.com/2009/09/34-how-to-set-up-web-blast-using.html">How to set up web blast using BioSlax</a></div>
<div>
33) <a href="http://bioinfotutlets.blogspot.com/2009/06/33-how-to-set-up-bioslax-laptop-servers.html">How to set-up the bioslax laptop servers</a></div>
<div>
32) <a href="http://bioinfotutlets.blogspot.com/2009/09/duplicates-finder-java-standalone.html">Duplicates Finder - a java standalone application to find sequence duplicates in your dataset</a></div>
<div>
31) <a href="http://bioinfotutlets.blogspot.com/2009/08/multiple-sequence-titles-in-same-blast.html">Multiple sequence titles in the same BLAST hit</a></div>
<div>
30) <a href="http://bioinfotutlets.blogspot.com/2009/08/30-using-vlookup-or-hlookup-in.html">Using VLOOKUP (or HLOOKUP) in Microsoft Excel</a></div>
<div>
29) <a href="http://bioinfotutlets.blogspot.com/2009/08/removing-sequences-that-are-full-gaps.html">Removing sequences that are fully gapped from alignment using BioEdit</a></div>
<div>
28) <a href="http://bioinfotutlets.blogspot.com/2009/07/28-how-to-import-tab-delimited-data.html">How to import tab delimited data into a table of a mySQL database in proline server???</a></div>
<div>
27) <a href="http://bioinfotutlets.blogspot.com/2009/06/27-how-to-create-metadata-file-for.html">How to create a metadata file for AVANA???</a></div>
<div>
26) <a href="http://bioinfotutlets.blogspot.com/2009/06/26-how-to-convert-alignment-file-aln-to.html">How to convert an alignment file (.aln) to a taln file (.taln)???</a></div>
<div>
25) <a href="http://bioinfotutlets.blogspot.com/2009/06/25-steps-for-obtaining-mutual.html">Steps for obtaining mutual information between two sequence alignments in AVANA</a></div>
<div>
24) <a href="http://bioinfotutlets.blogspot.com/2009/06/24-summary-steps-in-activating-lan.html">Summary steps in activating LAN connection in VMWare if problems still occur after post 22</a></div>
<div>
23) <a href="http://bioinfotutlets.blogspot.com/2009/06/how-to-use-mysql-in-proline.html">How to use MySQL in Proline Unix Server???</a></div>
<div>
22) <a href="http://bioinfotutlets.blogspot.com/2009/05/22-how-to-fix-your-internet-connection.html">How to fix your internet connection in BioSLAX VMWare</a></div>
<div>
21) <a href="http://bioinfotutlets.blogspot.com/2009/05/21-how-to-do-multiple-sequence.html">How to do multiple sequence alignment using MUSCLE</a></div>
<div>
20) <a href="http://bioinfotutlets.blogspot.com/2009/05/20-how-to-use-blastclust-to-identify.html">How to use Blastclust to identify representative sequences</a></div>
<div>
19) <a href="http://bioinfotutlets.blogspot.com/2009/05/19-how-to-remove-duplicate-sequences.html">How to remove duplicate sequences from a fasta formatted input file</a></div>
<div>
18) <a href="http://bioinfotutlets.blogspot.com/2009/05/18-how-to-shorten-description-line-in.html">How to shorten the description line in fasta format to just include GI number</a></div>
<div>
17) <a href="http://bioinfotutlets.blogspot.com/2009/05/17-installing-bioslax-as-full-linux.html">Installing BioSLAX as a full Linux system to your hard drive</a></div>
<div>
16) <a href="http://bioinfotutlets.blogspot.com/2009/05/16-lapis-converting-list-of-sequences.html">LAPIS: Fasta formatting a list of sequences</a></div>
<div>
15) <a href="http://bioinfotutlets.blogspot.com/2009/05/15-general-steps-that-you-need-to-do.html">General steps that you need to do after transferring the webpages from localhost to another server</a></div>
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14) <a href="http://bioinfotutlets.blogspot.com/2009/05/10-converting-phylip-file-to-alignment.html">How to convert a phylip file to an alignment file</a></div>
<div>
13) <a href="http://bioinfotutlets.blogspot.com/2009/05/13-how-to-create-bootable-usb.html">How to create a bootable (e.g. BioSLAX) USB thumbdrive</a></div>
<div>
12) <a href="http://bioinfotutlets.blogspot.com/2009/05/12-how-to-make-backup-of-live-cddvd.html">How to make a backup of Live CD/DVD</a></div>
<div>
11) <a href="http://bioinfotutlets.blogspot.com/2009/05/11-how-to-burn-iso-into-bootable-live.html">How to burn an ISO file (e.g. BioSlax.iso) into a bootable Live CD/DVD</a></div>
<div>
10) <a href="http://bioinfotutlets.blogspot.com/2009/05/bioslax-comprehensive-system-for.html">How to use/run the BioSlax Live CD</a></div>
<div>
9) <a href="http://bioinfotutlets.blogspot.com/2009/05/9-guide-to-using-bioslax.html">A Guide to Using BioSLAX</a></div>
<div>
8) <a href="http://bioinfotutlets.blogspot.com/2009/05/9-general-steps-to-do-after.html">General steps to do after transferring webpages from localhost to proline</a></div>
<div>
7) <a href="http://bioinfotutlets.blogspot.com/2009/05/7-setting-up-wwwblast-on-proline-server.html">Setting up wwwBlast on Proline Unix server</a></div>
<div>
6) <a href="http://bioinfotutlets.blogspot.com/2009/05/6-using-file-transfer-from-local.html">Using file transfer from local computer in Bioslax to another server</a></div>
<div>
5) <a href="http://bioinfotutlets.blogspot.com/2009/05/5-compressing-and-uncompressing-folder.html">Compressing and uncompressing a folder in Bioslax/Linux environment</a></div>
<div>
4) <a href="http://bioinfotutlets.blogspot.com/2009/05/4-exporting-sql-database-from-bioslax.html">Exporting SQL database from Bioslax and importing to another server's SQL database</a></div>
<div>
3) <a href="http://bioinfotutlets.blogspot.com/2009/05/3-generating-high-quality-publication.html">Generating High Quality Publication Figures</a></div>
<div>
2) <a href="http://bioinfotutlets.blogspot.com/2009/04/how-to-connect-to-remote-server-using.html">How to connect to remote server using the Konsole in BioSlax?</a></div>
<div>
1) <a href="http://bioinfotutlets.blogspot.com/2009/04/how-to-automate-blast-search-using.html">How To Automate BLAST Search using Network BLAST?</a></div>
</div>
</div>
Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.comtag:blogger.com,1999:blog-1737804828852994104.post-23340614445254462442009-06-10T17:03:00.003+08:002019-11-05T19:28:36.376+08:0026) How to convert an alignment file (.aln) to a taln file (.taln) for use in AVANA.It is important to note that the Antigenic Variability Analysis tool (AVANA) do not recognise a normal alignment file (.aln), and we need to convert it to a .taln format in order to do entropy or mutual information analysis. These are the steps to do it:<br />
<br />
a) Open the aln file in BioEdit. Make sure that the misalignments have been corrected.<br />
<br />
b) Click File\Export\tab-delimited text (title.tab.sequence)<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg4CpWjcvXBI_azfhVFxsctx50t9hz7lTQM6d9Evu2zWIQOPH4aDAJOfZ8wM2dVr0wduUvGbc-DsK7iMkGMJhXMK9nJGOEmCkgcXtz72lT3qwEBuJfYfuOdkMMNsLnaquQE79v9qYyxh_sE/s1600-h/taln1.jpg" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5345624265107346146" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg4CpWjcvXBI_azfhVFxsctx50t9hz7lTQM6d9Evu2zWIQOPH4aDAJOfZ8wM2dVr0wduUvGbc-DsK7iMkGMJhXMK9nJGOEmCkgcXtz72lT3qwEBuJfYfuOdkMMNsLnaquQE79v9qYyxh_sE/s400/taln1.jpg" style="cursor: hand; cursor: pointer; display: block; height: 258px; margin: 0px auto 10px; text-align: center; width: 400px;" /></a><br />
<br />
<br />
c) Change "Save as type" as "All Types", and name the file. Make sure to add ".taln" at the end of the filename, and save it to anywhere you want in your desktop.<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmUIfDZL905DFPxJwj0nSmWbiYgvj1pi96K3okuzL7ARC8w70XbwisfMx9aQ5DmNlxuAvInKj10vF0J7gI2Boof-FIaJztM0X56dkvqR7jqOoqfsRmaa6dsWm3EUJCeg2KAp_LpCyTUklj/s1600-h/taln2.jpg" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5345624757281020274" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmUIfDZL905DFPxJwj0nSmWbiYgvj1pi96K3okuzL7ARC8w70XbwisfMx9aQ5DmNlxuAvInKj10vF0J7gI2Boof-FIaJztM0X56dkvqR7jqOoqfsRmaa6dsWm3EUJCeg2KAp_LpCyTUklj/s400/taln2.jpg" style="cursor: hand; cursor: pointer; display: block; height: 258px; margin: 0px auto 10px; text-align: center; width: 400px;" /></a><br />
<br />
d) [ CAUTION! ] Open the ".taln" file in a text editor, scroll to the bottom of the page and delete the last line that shows the consensus sequence symbols. AVANA may or may not run when the input file contains these consensus symbols, however, the calculations reported by AVANA would be off by 1 as it would count the last line as an additional sequence.^BeNBeN^http://www.blogger.com/profile/11629878814774576609noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-52942646754911694222009-09-02T16:04:00.016+08:002019-11-03T15:02:36.534+08:0032) Duplicates Finder - a java standalone application to find sequence duplicates in your datasetProtein (Nucleotide) Sequences downloaded from NCBI Taxonomy Browser or other similar databases for an organism, in our case viruses, contain sequences which are duplicates of each other. Sometimes, these sequence duplicates turn out to be duplicate GenPept records, as found during our analyses, which need to be removed from the dataset to remove bias.<br />
<br />
One could use the ‘Remove duplicates’ function in Excel to do this; it returns the list of unique sequences. However, Excel does not do a good job when the dataset is large (large number or long sequences).<br />
<br />
Here, we provide a simple desktop application to extract the sets of duplicates from a dataset and also provide the list of unique sequences from the input dataset.<br />
<br />
<strong>How to use the program:</strong><br />
<br />
<ol>
<li>Download the zip file DuplicateFinder.zip <a href="https://www.dropbox.com/s/ddifkwihcbqgoi5/DuplicateFinder.zip?dl=0">here</a>. Extract contents to a desired location. </li>
<br />
<li>Click on the DuplicatesFinder.jar, the program starts and you are good to go. Since this is a java program, it is OS independent.<br />(NOTE: You need to have java runtime environment (JRE) installed in your system to run the program. To check if your system has java installed, refer to the end of this post.)</li>
</ol>
<br />
<strong>Input Files accepted by the program:</strong><br />
<ol>
<li>Comma separated values (*.csv)<br /><ul>
<li>The data should contain two colums – Identifier number, Sequence.<br />Identifier is a unique number to identify the sequence.<br />Sequence is the set of sequences to be analyzed.</li>
</ul>
</li>
<br />
<li>FASTA (*.fasta) or Tab delimited (*.txt)<br /><ul>
<li>The sequences should be in fasta format as shown below<br />>716349<br />uquiertyqyjej<br />quiejhieq<br />>837468<br />oiweirjtyiwj</li>
</ul>
</li>
</ol>
<br />
<strong>Output Files created by the program:</strong><br />
The output files are created in the same directory and folder as the input file.<br />
Two output files are created:<br />
<br />
<ol>
<li>Duplicates sequences File: A file containing the sets of duplicates (<inputfilename>Duplicates.csv). The columns in the file are:<br /><ul>
<li>Duplicate Set – the index of groups of duplicates;</li>
<br />
<li>Count – the index of a duplicate sequence in the set of duplicates it belongs to. So each series of numbers from 1 to n represents a set of sequence duplicates with a total of n duplicate sequences in that set;</li>
<br />
<li>Sequence – the duplicate sequences in ascending order (for easy visual checking).</li>
<br />
<li>Identifier – the number from the identifier column in the .csv file or the identifier number after '>' in the .fas and .txt files.</li>
<br />
<li>Remarks – remarks if any.</li>
</ul>
</inputfilename></li>
<br />
<li>Unique sequences file: A file containing the unique sequences from the dataset in fasta format (<inputfilename>Unique.fas). The file includes one representative from each set of duplicates.</inputfilename></li>
</ol>
<br />
<br />
NOTE: In both output files, the sequences are arranged in ascending order of the sequence.<br />
<br />
<strong>A Working Example</strong> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEga4HRKSTg9RxCn87LT5s9luBWDLVtdfWoKnF6tSrBmuCu2tZESyMzANXVt6vR-Z4ZrqXD-eJfvsHi1mBiiljYNavlXu314ddx0GXjobhHrK8Gt3EtteHokrattAJZ558UKJMctJDQ9Ewe4/s1600-h/InputFiles.JPG"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5376783455337964514" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEga4HRKSTg9RxCn87LT5s9luBWDLVtdfWoKnF6tSrBmuCu2tZESyMzANXVt6vR-Z4ZrqXD-eJfvsHi1mBiiljYNavlXu314ddx0GXjobhHrK8Gt3EtteHokrattAJZ558UKJMctJDQ9Ewe4/s320/InputFiles.JPG" style="cursor: hand; float: right; height: 269px; margin: 0px 0px 10px 10px; width: 309px;" /></a><br />
<ul>
<li>Input file with 3 unique sequences and 2 groups of duplicates<br />(Group 1 – 1A and 1B; Group 2 – 2A, 2B and 2C)</li>
<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHw-5IEFbu2piceqHJKchCkwWIxZdzVdvhi2evdIOrTGAXEgEbjxuUen3j5z8koy2r83aWKz-cmtVndqXQt0umHggQDK-VSD1BGejqCO5H1sJpkZQF5c_dOSAce6vdxOEyVPizg7wtXyf9/s1600-h/Program.JPG"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5376784941800913986" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHw-5IEFbu2piceqHJKchCkwWIxZdzVdvhi2evdIOrTGAXEgEbjxuUen3j5z8koy2r83aWKz-cmtVndqXQt0umHggQDK-VSD1BGejqCO5H1sJpkZQF5c_dOSAce6vdxOEyVPizg7wtXyf9/s320/Program.JPG" style="cursor: hand; cursor: pointer; float: right; height: 296px; margin: 0 0 10px 10px; width: 320px;" /></a><br />
<li>Start the Duplicate Finder program. Click ‘Open’. A file chooser with file filtering set to show only *.csv, *.fas or *.txt files pops up. Select your input file (here, Sample.fas). Click ‘Open’.</li>
<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjW-ApgaatW3yRKg7G5Qi0RyOreL_lhoJdYQeJCCwoLY4h0sX2AA4RSblNp4bG3XmTKz8YHe95bhcj_VcAzJCq2p1zoRx9uTILfFDlxhChoffoeEi3ZQMBaKAcR9RCajoP3vKeUPEllHJXF/s1600-h/Done.JPG"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5376785546662838818" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjW-ApgaatW3yRKg7G5Qi0RyOreL_lhoJdYQeJCCwoLY4h0sX2AA4RSblNp4bG3XmTKz8YHe95bhcj_VcAzJCq2p1zoRx9uTILfFDlxhChoffoeEi3ZQMBaKAcR9RCajoP3vKeUPEllHJXF/s320/Done.JPG" style="cursor: hand; cursor: pointer; float: right; height: 147px; margin: 0 0 10px 10px; width: 320px;" /></a><br />
<li>The path of your input file is set. Click ‘Generate results’. Wait for the confirmation window saying “Done” to indicate that your results have been generated. Click ‘OK’.</li>
<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjruCkIoSKcfg9fGN45rg2DLdWUR1V76JRMwBSDQwV2TdEZZm369Cv5iUF9pe7i9qUzrtUcJjoKWtPIMLk2uGdKw74ZdESFCnitC4HTM2LaNtm4IX7Brqfcv7ac_rQYWXllXLgvhKuStHf4/s1600-h/Results.JPG"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5376787219887196610" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjruCkIoSKcfg9fGN45rg2DLdWUR1V76JRMwBSDQwV2TdEZZm369Cv5iUF9pe7i9qUzrtUcJjoKWtPIMLk2uGdKw74ZdESFCnitC4HTM2LaNtm4IX7Brqfcv7ac_rQYWXllXLgvhKuStHf4/s320/Results.JPG" style="cursor: hand; cursor: pointer; float: right; height: 194px; margin: 0 0 10px 10px; width: 320px;" /></a><br />
<li>Go to the folder containing your input file. You will find two new files created with names <inputfilename>Duplicates.csv and <inputfilename>Unique.fas. In our case, our input file was Sample. So the results are SampleDuplicates.csv and SampleUnique.fas.</inputfilename></inputfilename></li>
<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguP6u2sUr55Qfry3rbdd2xyMKGmVquWpqq_ASZbtS9HYtRH-buIYW257X7H35xKM27Il0YXWnwuieK5LKBlhVcUzMx0O_QSu2mF50DUq6SPxrRaCiXuKN0DBmQcqz5cw0tDE_uwZPxFF8-/s1600-h/Duplicates.JPG"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5376789265695282946" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguP6u2sUr55Qfry3rbdd2xyMKGmVquWpqq_ASZbtS9HYtRH-buIYW257X7H35xKM27Il0YXWnwuieK5LKBlhVcUzMx0O_QSu2mF50DUq6SPxrRaCiXuKN0DBmQcqz5cw0tDE_uwZPxFF8-/s320/Duplicates.JPG" style="cursor: hand; cursor: pointer; float: right; height: 154px; margin: 0 0 10px 10px; width: 320px;" /></a><br />
<li><b>Output file 1: SampleDuplicates.csv</b><br /><u>Duplicate column:</u> index for groups of duplicates.<br />In our example, there were two groups of duplicates in the input file.<br /><u>Count column: </u>the index of a duplicate sequence in the group of duplicates it belongs to.<br />In our example, group 1 had two duplicate sequences – Duplicate1A and Duplicate1B – both of which are indicated in the Sequence column, followed by their identifier in the next column. Group 2 had three duplicate sequences – Duplicate2A, Duplicate2B and Duplicate2C – which are the three sequences indicated.<br /><u>Sequence column:</u> the duplicate sequences in ascending order (for easy visual checking).<br /><u>Identifier column:</u> the number from the identifier column in the .csv file or the identifier number after '>' in the .fas and .txt files</li>
<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjP0PVBKCuv0faMThcivq5h23xKIZ2En_pIIVucUexq_pLx6ho7S-D5aXYfIHoHtE3BUSvbQssNbymrJCdO_FibS_1O1Tpuk-oM-bfrfBHoa3TbqYGMtyc-fL41tyx41TeFHK5pcj0I20Kg/s1600-h/Unique.JPG"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5376789628869004962" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjP0PVBKCuv0faMThcivq5h23xKIZ2En_pIIVucUexq_pLx6ho7S-D5aXYfIHoHtE3BUSvbQssNbymrJCdO_FibS_1O1Tpuk-oM-bfrfBHoa3TbqYGMtyc-fL41tyx41TeFHK5pcj0I20Kg/s320/Unique.JPG" style="cursor: hand; cursor: pointer; float: right; height: 141px; margin: 0 0 10px 10px; width: 320px;" /></a><br />
<li><b>Output file 2: SampleUnique.fas</b><br />This file contains the set of unique sequences from the input dataset in fasta format. The set of unique sequences includes one representative from each set of duplicates, usually the first one in the set of duplicates.<br />In our example, we have 3 unique sequences – Unique1, Unique2 and Unique3 – which are present in the output file. In addition, the output also contains one representative from each set of duplicates – Duplicate1A from the first set and Duplicate2A from the second set.</li>
</ul>
<br />
<br />
<b>To check if your system has JRE:</b><br />
<ol>
<li>Go to command prompt and type java –version. </li>
<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhe3Wt8g9LHeqeU-jOVu9sN2dHzD5B36lmZKyFhg9PpnhIhjmwmTLvN6EwHDH5MHJvhC35Oz2_GD_ekdw7Kv7I0UJdiLtbphqbC-flNpKoOnjZ-g9UMt7kEq9YhlmzdGgcfwrWjguTdfNM/s1600-h/java.JPG"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5376790352957345250" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhe3Wt8g9LHeqeU-jOVu9sN2dHzD5B36lmZKyFhg9PpnhIhjmwmTLvN6EwHDH5MHJvhC35Oz2_GD_ekdw7Kv7I0UJdiLtbphqbC-flNpKoOnjZ-g9UMt7kEq9YhlmzdGgcfwrWjguTdfNM/s320/java.JPG" style="cursor: hand; cursor: pointer; float: right; height: 74px; margin: 0 0 10px 10px; width: 320px;" /></a><br />
<li>If your system has java, you will see the version details similar to one shown:</li>
</ol>
<br />
<br />
a) If your system does not have java installed, you get the error:<br />
‘java’ is not recognized as an internal or external command, operable program or batch file.<br />
b) You can then download the JRE for your OS from Sun Microsystems: http://www.java.com/en/download/manual.jsp)<br />
<div>
<br /></div>
<div>
=UPDATE=</div>
<div>
<br /></div>
<div>
This program is only able to remove exact EQUAL LENGTH duplicate sequences; it does not treat subset duplicates as duplicates. For example, let's say we have the following sequences:</div>
<div>
<br /></div>
<div>
<div>
>1</div>
<div>
AAAAAAAAA</div>
<div>
>2</div>
<div>
AAAAAAAA</div>
<div>
>3</div>
<div>
AAAAAAAA</div>
</div>
<div>
<br /></div>
<div>
The output of unique sequences from the program are:</div>
<div>
<br /></div>
<div>
<div>
<div>
>1</div>
<div>
AAAAAAAAA</div>
</div>
<div>
>2</div>
<div>
AAAAAAAA</div>
<div>
<br /></div>
</div>
<div>
You can see that though >2 is a subset duplicate of >1, the program still considers it as unique because it only removes exact same length duplicate sequences, such as >2 and >3, where one was removed and the other kept.</div>
<div>
<br /></div>
<div>
What happens if you have gaps in your input sequences? Let's say we have the following input sequences:</div>
<div>
<br /></div>
<div>
<div>
>1</div>
<div>
AAAAAAAAA</div>
<div>
>2</div>
<div>
AAAAAAAA-</div>
<div>
>3</div>
<div>
AAAAAAAA-</div>
<div>
>4</div>
<div>
AAAAAAAAAB</div>
<div>
>5</div>
<div>
AAAAAAAAAB</div>
<div>
>6</div>
<div>
AAAAAAAAAC</div>
</div>
<div>
<br /></div>
<div>
The output that you get from the program is:</div>
<div>
<br /></div>
<div>
<div>
>2</div>
<div>
AAAAAAAA-</div>
<div>
>1</div>
<div>
AAAAAAAAA</div>
<div>
>4</div>
<div>
AAAAAAAAAB</div>
<div>
>6</div>
<div>
AAAAAAAAAC</div>
</div>
<div>
<br /></div>
<div>
Just like in the previous example, only exact equal length duplicates are removed and the gap is treated like an amino acid. So, if you do not want gaps to affect the removal of duplicates (especially if they are in the middle of the sequences), you should remove them using the simple replace function in most text editors (replace "-" with nothing).</div>
<div>
<br /></div>
<div>
So what if you are interested in removing subset duplicates? What program can you use?</div>
<div>
You can use Jalview and a tutorial is available <a href="http://bioinfotutlets.blogspot.com/2009/05/19-how-to-remove-duplicate-sequences.html">here</a>.</div>
<div>
<br /></div>
<div>
<span class="Apple-style-span" style="color: rgb(51 , 51 , 51); font-size: 13px; line-height: 20px;"><i>Content by: Rashmi & Asif M. Khan<br />Posted by: Rashmi<br />Edited by: Asif M. Khan</i></span></div>
Unknownnoreply@blogger.com13tag:blogger.com,1999:blog-1737804828852994104.post-83951533384579155502009-04-02T00:44:00.007+08:002011-03-21T10:50:45.778+08:001) How To Automate BLAST Search using Network BLAST?<div>===Update: 20 March, 2011===</div><div><br />
</div><div>Question to NCBI: </div><div>NCBI will no longer produce newer versions of NetBLAST?</div>Is the legacy version still supported?<br />
<div><br />
</div><div>Reply from NCBI:<br />
<div><br />
</div><div>"NetBLAST was rewritten into blast+ as the "-remote" option, so it will be maintained there. Legacy blast (blastall, blastcl3, etc.) is still being supported, but that will stop at some, unknown point in the future. I'd guess it will be supported for at least another year. That does not mean that we will address all bugs, particularly for blastcl3 (NetBLAST)."<br />
<div><span class="Apple-style-span" style="font-family: Helvetica; font-size: medium;"></span></div></div><div><br />
</div><div>=======================</div><div><br />
</div>One can use Blastcl3,<a href="" id="blast2" name="blast2"></a> the NCBI BLAST network client, to remotely connect to the NCBI BLAST servers to run automated BLAST searches. No web browser is required, you don't have to wait in front of the computer for the results and can perform "batch" search of many sequences against the databases at one time. The results of the search using this Network Blast will be identical to that of the Web version (http://blast.ncbi.nlm.nih.gov/Blast.cgi), as long as the identical parameters are used. I have tried and tested this.<br />
<br />
<span style="font-style: italic;">Note on blast parametes for users who will rely on the Web version for the parameters to be used on the Network version:</span><br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWwEfRL-Yw5qLR-GmMozi2cZtQEJfp_xXMyFQtXJeHr5AZgG-w0RBxm-LzewvU09-mXFsniVrasTML6JUHHzbWkoNdRMQoWZD4uVvLl0NiiQasIEktnn284ZYHISrzpmhbHWr5RePjBQTh/s1600-h/BlastSearchParam.png" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5296045448171605618" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWwEfRL-Yw5qLR-GmMozi2cZtQEJfp_xXMyFQtXJeHr5AZgG-w0RBxm-LzewvU09-mXFsniVrasTML6JUHHzbWkoNdRMQoWZD4uVvLl0NiiQasIEktnn284ZYHISrzpmhbHWr5RePjBQTh/s400/BlastSearchParam.png" style="cursor: pointer; height: 400px; width: 365px;" /></a><br />
<br />
If you don't uncheck (untick) the option for short sequence queries ("<label class="right inlinelabel" for="adjparam">Automatically adjust parameters for short input sequences"</label>) on the Web version, the default algorithm parameters that are displayed on the input page will not be used (for example, E-value of 10, Blosum 62 matrix, Word size 2, etc). This I think is a bug because it does not make sense showing the default parameters if they are not going to be used, especially when the short queries option is checked by default. Ideally, they should have not checked the short queries option and if it is checked by the user, the resulting default parameters should be shown.<br />
<br />
So, if you don't plan to use the short queries option, just uncheck it and the parameters displayed will be used for the search; you can change them if you like. If you are happy with what you get on the results page, then take note of the parameters and then set them for use by the Network Blast.<br />
<br />
Now, for those who plan to use the short queries option, do the following:<br />
<br />
1. Don't bother modifying the default algorithm parameters and click on the submit button.<br />
2. On the results page, click on the "Edit and Resubmit" button to find out what algorithm parameters were used for the search. The parameters that you see on the resulting page, were the exact values that were used for the search. If you are happy with the blast result, you can stick with these parameters, otherwise, you are free to modify them. If you plan to modify them, make sure you uncheck the option for short queries in order for your changes to be effective, otherwise, the default parameters for short queries that were displayed on that page will still be used. Once you are satisfied with your final set of parameters, take note of them and then set them for use by the Network Blast.<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiL_GfS2mbiBWFS8ZQNCeADEEheqycr8WN_hwJ95AxJmmMjFsefoEOZJi1vWDJ7kpSlHtutMsQvQgeXoR8cuicjjilJAw9aGvqQRVco6D7RluLamSp1Cnsql-1zD2pwHJNAjQzkOGbNJ9e8/s1600-h/Picture+1.png" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5296044021635613346" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiL_GfS2mbiBWFS8ZQNCeADEEheqycr8WN_hwJ95AxJmmMjFsefoEOZJi1vWDJ7kpSlHtutMsQvQgeXoR8cuicjjilJAw9aGvqQRVco6D7RluLamSp1Cnsql-1zD2pwHJNAjQzkOGbNJ9e8/s400/Picture+1.png" style="cursor: pointer; height: 181px; width: 400px;" /></a><br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGKF2F33KDX-T55ov4FjewsKpgwzkFeq0tJjIDKP569X3LZ-gp7jf3xhFAnr5uHZrIfBHZis3v8Gd3W_q8YadfhQnjQRake2EGaaWhbO6l4wJglO0_BwAOcilbRrnaDx43O6Hq7ksUiT-L/s1600-h/Picture+2.png" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5296044416811330514" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGKF2F33KDX-T55ov4FjewsKpgwzkFeq0tJjIDKP569X3LZ-gp7jf3xhFAnr5uHZrIfBHZis3v8Gd3W_q8YadfhQnjQRake2EGaaWhbO6l4wJglO0_BwAOcilbRrnaDx43O6Hq7ksUiT-L/s400/Picture+2.png" style="cursor: pointer; height: 245px; width: 400px;" /></a><br />
<br />
== Where to get Network Blast ==<br />
<br />
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.17/<br />
File: netblast-2.2.17-ia32-freebsd.tar.gz 2334 KB 8/26/2007 4:09:00 PM<br />
File: netblast-2.2.17-ia32-linux.tar.gz 2758 KB 8/26/2007 4:13:00 PM<br />
File: netblast-2.2.17-ia32-solaris.tar.gz 2416 KB 8/27/2007 8:10:00 PM<br />
File: netblast-2.2.17-ia32-solaris9.tar.gz 2455 KB 8/26/2007 4:15:00 PM<br />
File: netblast-2.2.17-ia32-win32.exe 1479 KB 8/22/2007 9:40:00 PM<br />
File: netblast-2.2.17-ia64-linux.tar.gz 5319 KB 11/1/2007 12:23:00 PM<br />
File: netblast-2.2.17-mips64-irix.tar.gz 4340 KB 8/26/2007 4:17:00 PM<br />
File: netblast-2.2.17-sparc64-solaris.tar.gz 4448 KB 8/26/2007 4:41:00 PM<br />
File: netblast-2.2.17-universal-macosx.tar.gz 4398 KB 8/26/2007 4:25:00 PM<br />
File: netblast-2.2.17-x64-linux.tar.gz 2834 KB 8/26/2007 4:13:00 PM<br />
File: netblast-2.2.17-x64-solaris.tar.gz 3287 KB 8/27/2007 8:27:00 PM<br />
File: netblast-2.2.17-x64-win64.exe 1686 KB 8/19/2007 4:29:00 AM<br />
<br />
For other methods, see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.pdf<br />
and http://www.ncbi.nlm.nih.gov/blast/blast_overview.shtml<br />
and the query.fcgi pages on how to construct an api to talk to various NCBI queries, e.g. automating the retrieval of GI numbers in FASTA or whatever formats.<br />
<br />
== How to run Network Blast in Linux OS (e.g BioSlax)==<br />
<pre>tar -zxvf netblast-2.2.17-ia32-linux.tar.gz
</pre><br />
<br />
* The following will be untarred (unzipped): VERSION bin/ data/ doc/<br />
* Blastcl3 is found in the bin folder<br />
<br />
== Example of how to run Network Blast ==<br />
<br />
1. Split the input fasta file (containing multiple sequences) into multiple files, with one sequence per file, using the command csplit. For example:<br />
<pre>csplit -n 1 multiple.fasta /\>/ \{\*\}
</pre><br />
<br />
The above command adds digits to names of the output fasta files without the padding of zeros infront.<br />
<br />
* Example of content of the input fasta file:<br />
>1<br />
ESWILRNPGYALVA<br />
>2<br />
GCGLFGKGSIDTCA<br />
<br />
..etc..<br />
<br />
* Examples of output files:<br />
<br />
file name: xx1<br />
content of xx1:<br />
>1<br />
ESWILRNPGYALVA<br />
<br />
file name: xx2<br />
content of xx2:<br />
>2<br />
GCGLFGKGSIDTCA<br />
<br />
.<br />
.<br />
.<br />
<br />
file name: xx10<br />
content of xx10:<br />
>10<br />
GCGLFGKGSIDTCA<br />
<br />
and so on to the last sequence ...<br />
<br />
<br />
2. Create an executable file containing the following code (relevant for queries of short length):<br />
<pre>for i in xx*
do
blastcl3 -p blastp -d nr -i $i -F F -e 200000 -I T -v 0 -b 20000
-f 11 -W 2 -T F -u "All[FILTER] NOT Viruses[ORGN] NOT
txid81077[ORGN]" -C F -M PAM30 -o $i.out
sleep 10
done
</pre><br />
<br />
'''NOTE:'''<br />
* xx refers to the name of the input files, for example xx1, xx2, etc<br />
* Sleep 10 is the time gap (10 seconds) between the end of one submission and the start of the next. This can be changed to longer time periods (recommended) in order not to overload the NCBI server. Otherwise, they may black list your IP.<br />
* -p is blast p program, -d nr is the NR database, -i is for input filename, -F F for false is to switch off low complexity and other filters, -I T set to true is to show the GI numbers in the definition lines, and -v 0 is to set number of database sequences to show one-line descriptions, -b is to list out 20000 hits, -f 11 threshold for extending hits, -W 2 set word size for short sequence queries, default used if set to zero (blastn 11, megablast 28, all others 3, and 2 for short queries), -T F to produce text output, instead of HTML, -u "Root[ORGN] NOT txid11082[Organism:exp] NOT txid81077[ORGN]" is to restrict search of database to results of Entrez2 lookup [String], -C F to not use composition-based statistics for blastp or tblastn (0 or F or f: no composition-based statistics), -M PAM30 select matrix for short sequence queries (BLOSUM62 for normal protein searches), and -o to specify output filename.<br />
<br />
<br />
3. Change the mode of the executable file in order to be able to execute. For example:<br />
<pre>chmod 755 x
</pre><br />
* x refers to the name of the executable file.<br />
* For more information, see [http://en.wikipedia.org/wiki/Chmod Chmod]and [http://www.xaviermedia.com/documents/chmod755.php Chmod755].<br />
<br />
<br />
4. Run the executable file. For example:<br />
<pre>./x
</pre><br />
* x refers to the name of the executable file<br />
<br />
A task can usually be started and run as a background task by putting a '&' at the end of the command line. For example:<br />
<pre>./x &
</pre><br />
<br />
If a task was started and is running in the foreground, it is still possible to move it to the background without cancelling it. To move a task from the foreground to the background perform the following steps:<br />
<br />
1. CTRL-Z (That is, while holding the CTRL key down, tap the 'z' key) This will suspend the current foreground job (task).<br />
2. Enter the job control command 'bg'<br />
3. Tap the 'Enter' key<br />
<br />
The job is now running in the background.<br />
<br />
Useful commands to see which jobs are still running is the 'jobs' or the 'ps ua' commands. If the 'jobs' command is used, a background jobs can be brought to the foreground with the command fg n where n is the job (not the PID) number.<br />
<br />
==Manual pages of Network Blast==<br />
<pre>blastcl3 2.2.17 arguments:
-p Program Name [String]
-d Database [String]
default = nr
-i Query File [File In]
default = stdin
-e Expectation value (E) [Real]
default = 10.0
-m alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular,
9 tabular with comment lines
10 ASN, text
11 ASN, binary [Integer]
default = 0
range from 0 to 11
-o BLAST report Output File [File Out] Optional
default = stdout
-F Filter query sequence (DUST with blastn, SEG with others) [String]
default = T
-G Cost to open a gap (-1 invokes default behavior) [Integer]
default = -1
-E Cost to extend a gap (-1 invokes default behavior) [Integer]
default = -1
-X X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
default = 0
-I Show GI's in deflines [T/F]
default = F
-q Penalty for a nucleotide mismatch (blastn only) [Integer]
default = -3
-r Reward for a nucleotide match (blastn only) [Integer]
default = 1
-v Number of database sequences to show one-line descriptions for (V) [Integer]
default = 500
-b Number of database sequence to show alignments for (B) [Integer]
default = 250
-f Threshold for extending hits, default if zero
blastp 11, blastn 0, blastx 12, tblastn 13
tblastx 13, megablast 0 [Real]
default = 0
-g Perform gapped alignment (not available with tblastx) [T/F]
default = T
-Q Query Genetic code to use [Integer]
default = 1
-D DB Genetic code (for tblast[nx] only) [Integer]
default = 1
-a Number of processors to use [Integer]
default = 1
-O SeqAlign file [File Out] Optional
-J Believe the query defline [T/F]
default = F
-M Matrix [String]
default = BLOSUM62
-W Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer]
default = 0
-z Effective length of the database (use zero for the real size) [Real]
default = 0
-K Number of best hits from a region to keep (off by default, if used a value of 100 is recommended) [Integer]
default = 0
-P 0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer]
default = 0
-Y Effective length of the search space (use zero for the real size) [Real]
default = 0
-S Query strands to search against database (for blast[nx], and tblastx)
3 is both, 1 is top, 2 is bottom [Integer]
default = 3
-T Produce HTML output [T/F]
default = F
-u Restrict search of database to results of Entrez2 lookup [String] Optional
-U Use lower case filtering of FASTA sequence [T/F] Optional
-y X dropoff value for ungapped extensions in bits (0.0 invokes default behavior)
blastn 20, megablast 10, all others 7 [Real]
default = 0.0
-Z X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)
blastn/megablast 50, tblastx 0, all others 25 [Integer]
default = 0
-R RPS Blast search [T/F]
default = F
-n MegaBlast search [T/F]
default = F
-L Location on query sequence [String] Optional
-A Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer]
default = 0
-w Frame shift penalty (OOF algorithm for blastx) [Integer]
default = 0
-t Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments. (0 invokes default behavior; a negative value disables linking.) [Integer]
default = 0
-C Use composition-based statistics for blastp or tblastn:
As first character:
D or d: default (equivalent to T)
0 or F or f: no composition-based statistics
1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001
2: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
For programs other than tblastn, must either be absent or be D, F or 0.
As second character, if first character is equivalent to 1, 2, or 3:
U or u: unified p-value combining alignment p-value and compositional p-value in round 1 only
[String]
default = D
-s Compute locally optimal Smith-Waterman alignments (This option is only
available for gapped tblastn.) [T/F]
default = F
</pre></div>Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-56628286061728119292009-05-13T12:31:00.013+08:002011-03-21T10:49:18.516+08:0019) How to remove duplicate sequences from a fasta formatted input file===Update: 21 March 2011===<br />
<br />
For a more comprehensive and updated information on this, please see <a href="http://bioinfotutlets.blogspot.com/2009/09/duplicates-finder-java-standalone.html">Post 32</a>.<br />
Read all the way to the end of that post.<br />
<br />
======================<br />
<br />
You can use Jalview to easily check for duplicates and remove them if any.<br />
<br />
1. Download and install Jalview on your home system from<br />
<br />
http://www.jalview.org/download.html<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi690SXPXvbz3f5Y0GzUXj8vKuWRlvDDbVXcDEbLSY2_yf1nlsHIS2mB9UIzSDt7l6_PrV8hkjEjAYKFU5XM_3MBKAGyWFYIpdc-6eMGE_ap128IFllUZklnKQ4E_UNviHYd8MXEO72Xkl5/s1600-h/image002.jpg"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5335162611626802018" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi690SXPXvbz3f5Y0GzUXj8vKuWRlvDDbVXcDEbLSY2_yf1nlsHIS2mB9UIzSDt7l6_PrV8hkjEjAYKFU5XM_3MBKAGyWFYIpdc-6eMGE_ap128IFllUZklnKQ4E_UNviHYd8MXEO72Xkl5/s400/image002.jpg" style="cursor: hand; cursor: pointer; height: 229px; width: 400px;" /></a><br />
<br />
<br />
2. Run Jalview and close all example windows<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjm9UJK-MQphLIjC8xmjhtlzCzA06_tujwVFNxwvXS6wD3f0AbEKkF-DSj72QYW6hVoBaJlJ-G3WexFfS3hYlADgi0CV5iIUvkiYneCEbi7Tu-M_JACO4I7wkK9n8FBDfniTXSvTk1s5ff4/s1600-h/image004.jpg"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5335162680792443026" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjm9UJK-MQphLIjC8xmjhtlzCzA06_tujwVFNxwvXS6wD3f0AbEKkF-DSj72QYW6hVoBaJlJ-G3WexFfS3hYlADgi0CV5iIUvkiYneCEbi7Tu-M_JACO4I7wkK9n8FBDfniTXSvTk1s5ff4/s400/image004.jpg" style="cursor: hand; cursor: pointer; height: 244px; width: 400px;" /></a><br />
<br />
3. Load your fasta file to Jalview<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7z80uul8tRbdCjFcCK7mO1MAUyjToarhvm4K1cHPDHczF9GuDxooLk4me1mrfThf4eL5DYyDOTh_B41gOiMr3B_hyBK3kZPHL34RKTu14Wnjby8drz49AVc8qRtcL_iaSpIO4v1UDUGsv/s1600-h/image006.jpg"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5335162782818896546" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7z80uul8tRbdCjFcCK7mO1MAUyjToarhvm4K1cHPDHczF9GuDxooLk4me1mrfThf4eL5DYyDOTh_B41gOiMr3B_hyBK3kZPHL34RKTu14Wnjby8drz49AVc8qRtcL_iaSpIO4v1UDUGsv/s400/image006.jpg" style="cursor: hand; cursor: pointer; height: 270px; width: 400px;" /></a><br />
<br />
<br />
4. Remove duplicates: <br />
<br />
- Select all sequence<br />
<br />
- Go ‘Edit’ to uncheck the pad gaps function.<br />
<br />
- In ‘Edit’, select ‘Remove all gaps’<br />
<br />
- After that select ‘Remove redundancy’<br />
<br />
- At the “redundancy threshold selection” dialog box, set the threshold value to 100, click ‘Remove’.<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjsSYIwrjg0ztO5DRA9tozs7GLBnrUFKxlfADF5ft1HpOAIXZAWHhHfz6PJa0VGFQZ6SjU_kuKgvxC1PJ19ceJaIVKRBg2nK0OG-kgjhyphenhyphensoxY_-OrGMi_huuohZuHbU_Tlw0Hd8CtVXdYgw/s1600-h/image008.jpg"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5335162900899906642" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjsSYIwrjg0ztO5DRA9tozs7GLBnrUFKxlfADF5ft1HpOAIXZAWHhHfz6PJa0VGFQZ6SjU_kuKgvxC1PJ19ceJaIVKRBg2nK0OG-kgjhyphenhyphensoxY_-OrGMi_huuohZuHbU_Tlw0Hd8CtVXdYgw/s400/image008.jpg" style="cursor: hand; cursor: pointer; height: 262px; width: 400px;" /></a><br />
<br />
5. Saving the unique fasta file and you are done!<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJJkqICLolGLvN-Ivg5G7EfDpn8U-dJXcBxTI9jZFZBPpNiPPMLbhw60sKAFNnxX7r8Lii6VwJQz0yx4KI6-WfYYzyIrWFYR3D3WnXMIkeJ0Sla55rWEUEE6exEwjAKXilyOJEvPJGUwo5/s1600-h/image010.jpg"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5335163044064172114" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJJkqICLolGLvN-Ivg5G7EfDpn8U-dJXcBxTI9jZFZBPpNiPPMLbhw60sKAFNnxX7r8Lii6VwJQz0yx4KI6-WfYYzyIrWFYR3D3WnXMIkeJ0Sla55rWEUEE6exEwjAKXilyOJEvPJGUwo5/s400/image010.jpg" style="cursor: hand; cursor: pointer; height: 178px; width: 400px;" /></a><br />
<br />
<i><br />
Content by: Asif M. Khan & Sye Bee<br />
Posted by: Sye Bee<br />
Edited by: Asif M. Khan<br />
</i>cbeehttp://www.blogger.com/profile/13749285444941751919noreply@blogger.com3tag:blogger.com,1999:blog-1737804828852994104.post-55516603026288599102010-08-27T16:40:00.004+08:002011-01-24T04:56:17.507+08:0040) How to include my own database ID along with the NCBI ID on the BLAST's result page?1. Edit the sequence header as shown to include your own database id (eg.STAT_00044 from my database) in the fasta file<br /><br />>gi|34392270|emb|CAE46396.1| STAT_00044 Dd-STATb protein [Dictyostelium discoideum]<br /><br />2. formatdb<br /><br />formatdb -i input.fasta -p T -o T<br /><br />3. In the /usr/local/wwwblast-2.2.17 folder of BioSLAX, backup blast.html and blast.cgi<br /><br />4. Change the content of blast.cgi as shown (pipe the output of blast.REAL and do sed to get the hyperlink of your own database Id included in the blast result)<br /><br />#!/bin/csh -f<br /><br />#<br /># $Id: blast.cgi,v 1.1 2002/08/06 19:03:51 dondosha Exp $<br />#<br /><br />echo "Content-type: text/html"<br />echo ""<br /><br />#setenv DEBUG_COMMAND_LINE TRUE<br />setenv BLASTDB db<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEic0-HYqyAGpqEEwu6_0cmu0DdO7KcG8jiW3nZCJTXky-bSRIWqFCpzscXkv5GHhDEIOt5lCBOAmjeJ_7V95mKfJ3AWr5r3HPbcPY9fcKZ_q4UhiQYzuMxY8Ds3H45YKxyTQ8m1S7byslU/s1600/code_new.jpg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 400px; height: 61px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEic0-HYqyAGpqEEwu6_0cmu0DdO7KcG8jiW3nZCJTXky-bSRIWqFCpzscXkv5GHhDEIOt5lCBOAmjeJ_7V95mKfJ3AWr5r3HPbcPY9fcKZ_q4UhiQYzuMxY8Ds3H45YKxyTQ8m1S7byslU/s400/code_new.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5510013022667394930" /></a><br /><br /><br /><br /># I used my own database STATdb_Id as an example below.<br /><br />5. Output example<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_v02gAcjUqcXps79RfM4Di2qInD8HPQy_ZHqtu97ABUtHJIbYYTumxgxXBESKC753sINesNAjLpJv5GUHkJwOxJzz4WAriED8zHsgt2R6DzSXE7vwThgnLT0RT1v0aoittrDHvLITDcQ/s1600/blast_hit.jpg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 400px; height: 327px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_v02gAcjUqcXps79RfM4Di2qInD8HPQy_ZHqtu97ABUtHJIbYYTumxgxXBESKC753sINesNAjLpJv5GUHkJwOxJzz4WAriED8zHsgt2R6DzSXE7vwThgnLT0RT1v0aoittrDHvLITDcQ/s400/blast_hit.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5510010727108601858" /></a>Pawanhttp://www.blogger.com/profile/10674070824859904556noreply@blogger.com2tag:blogger.com,1999:blog-1737804828852994104.post-87909703701915695122010-03-11T20:40:00.001+08:002010-03-11T20:47:28.876+08:0039) How To Create a Password Protected Website<a title="View howtocreateapasswordprotectedwebsite on Scribd" href="http://www.scribd.com/doc/28200441/howtocreateapasswordprotectedwebsite" style="margin: 12px auto 6px auto; font-family: Helvetica,Arial,Sans-serif; font-style: normal; font-variant: normal; font-weight: normal; font-size: 14px; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none; display: block; text-decoration: underline;">howtocreateapasswordprotectedwebsite</a> <object id="doc_219080002969192" name="doc_219080002969192" height="600" width="100%" type="application/x-shockwave-flash" data="http://d1.scribdassets.com/ScribdViewer.swf" style="outline:none;"> <param name="movie" value="http://d1.scribdassets.com/ScribdViewer.swf"> <param name="wmode" value="opaque"> <param name="bgcolor" value="#ffffff"> <param name="allowFullScreen" value="true"> <param name="allowScriptAccess" value="always"> <param name="FlashVars" value="document_id=28200441&access_key=key-14wgwvjhr7ms3zlr0zl7&page=1&viewMode=list"> <embed id="doc_219080002969192" name="doc_219080002969192" src="http://d1.scribdassets.com/ScribdViewer.swf?document_id=28200441&access_key=key-14wgwvjhr7ms3zlr0zl7&page=1&viewMode=list" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" height="600" width="100%" wmode="opaque" bgcolor="#ffffff"></embed> </object>Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-86902331068657440312010-03-08T03:58:00.003+08:002010-03-08T04:01:33.739+08:0038) Running Blast+ client on Mac OSX<a title="View runningblast+clientonmac on Scribd" href="http://www.scribd.com/doc/27979707/runningblast-clientonmac" style="margin: 12px auto 6px; font-family: Helvetica,Arial,Sans-serif; font-style: normal; font-variant: normal; font-weight: normal; font-size: 14px; line-height: normal; font-size-adjust: none; font-stretch: normal; display: block; text-decoration: underline;">runningblast+clientonmac</a> <object id="doc_606417843747479" name="doc_606417843747479" type="application/x-shockwave-flash" data="http://d1.scribdassets.com/ScribdViewer.swf" style="outline-color: -moz-use-text-color; outline-style: none; outline-width: medium;" height="600" width="100%"> <param name="movie" value="http://d1.scribdassets.com/ScribdViewer.swf"> <param name="wmode" value="opaque"> <param name="bgcolor" value="#ffffff"> <param name="allowFullScreen" value="true"> <param name="allowScriptAccess" value="always"> <param name="FlashVars" value="document_id=27979707&access_key=key-2m523e9v840ypmz8ta2q&page=1&viewMode=list"> <embed id="doc_606417843747479" name="doc_606417843747479" src="http://d1.scribdassets.com/ScribdViewer.swf?document_id=27979707&access_key=key-2m523e9v840ypmz8ta2q&page=1&viewMode=list" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" wmode="opaque" bgcolor="#ffffff" height="600" width="100%"></embed> </object>Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-66245288413581417562009-12-14T19:52:00.020+08:002009-12-15T20:10:26.151+08:0037) LAPIS: Converting blast hit sequences into fasta formatLAPIS is an Open Source software written in JAVA. One of its uses is to make data presentation simpler for analysis by extracting suitable information from a text file.<br /><br />For example, it can be used to extract only the subject and the identifier (NCBI GI number) information from a BLAST result. Below is an illustration of how this can be done using LAPIS:<br /><br /><span style="font-weight: bold;">Before</span><br /><br />>gi|126385999|gb|CP000521.1| Acinetobacter baumannii ATCC 17978, complete genome<br />Length = 3976747<br /><br />Score = 570 bits (1470), Expect = e-163<br />Identities = 284/284 (100%), Positives = 284/284 (100%)<br />Frame = -2<br /><span style="font-size:100%;"><br /></span><span style="font-size:100%;">Query: </span><span style="font-size:100%;">1 </span><span style="font-size:100%;"><span type="courier" new="">LNFKFNFISLMNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHT </span></span><span style="font-size:100%;">60<br /></span> <span style="font-size:100%;">LNFKFNFISLMNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHT<br /></span><span style="font-size:100%;">Sbjct: </span><span style="font-size:100%;">1766322 </span><span style="font-size:100%;">LNFKFNFISLMNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHT </span><span style="font-size:100%;">1766143<br /><br /></span><br /><span style="font-weight: bold;">After</span><br /><br />>gi|126385999<br />LNFKFNFISLMNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHT<br /><br /><span style="font-weight: bold;">Methodology:</span><br />1. Select the line containing the fasta description together with the line containing the subject sequences: “line containing > or line containing sbjct” ->Tools ->Extract<br />2. To get rid of the numbers in the line containing sbjct: “digits in line containing sbjct” ->Tools -> Omit<br />3. To get rid of sbjct: “sbjct:” -> Extract -> Omit<br />4. To get rid of dashes: type “-" -> Extract -> Omit<br />5. To get rid of the extra spaces in the lines containing sequences: “spaces not in line containing >” -> Tools -> Omit<br />6. In case you want to clean up the description line to only have the GI<br /> From second | in line containing > to start of linebreak<br /><br /><br /><span style="font-weight: bold;">Screen shots: The following screen shots shows the input and the output at each step</span><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgaqXnPyrv3RRHyGvnU0o_35Y6mypw90YXIPV8hKCvdnNoNcuRL7Xbt1AB1s0nOZlsyTfZ4WTc7juiK7TT-5mRbOM53vPxsHbkEO-11avzzi0dNokby9FQYqnIv3jlMkE7uC3_F-CqHjFQ/s1600-h/Lapis_1.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 151px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgaqXnPyrv3RRHyGvnU0o_35Y6mypw90YXIPV8hKCvdnNoNcuRL7Xbt1AB1s0nOZlsyTfZ4WTc7juiK7TT-5mRbOM53vPxsHbkEO-11avzzi0dNokby9FQYqnIv3jlMkE7uC3_F-CqHjFQ/s400/Lapis_1.bmp" alt="" id="BLOGGER_PHOTO_ID_5415060326560928482" border="0" /></a><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />For extracting specific information, the user needs to find a pattern and type it in the pattern box as shown below:<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDuOvsEcWD-waSd6ajNFDim02EMk8VVkAxX4NUYfOn79vu86r3BiuBcC7rVHIvvbbG1yvq-tWYJ3XVjnfPScPF3sHuJKQ0koJ7NEYRuaeUxBhlCOIvqIh8_qnmbAfUVk9bQ3IBzqFpXMw/s1600-h/Lapis_2.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 198px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDuOvsEcWD-waSd6ajNFDim02EMk8VVkAxX4NUYfOn79vu86r3BiuBcC7rVHIvvbbG1yvq-tWYJ3XVjnfPScPF3sHuJKQ0koJ7NEYRuaeUxBhlCOIvqIh8_qnmbAfUVk9bQ3IBzqFpXMw/s400/Lapis_2.bmp" alt="" id="BLOGGER_PHOTO_ID_5415060979950138578" border="0" /></a><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />The pattern above is used to extract the two necessary lines for the further analysis.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivjV9lKp-ORXOXFAM70n6kiWuZ5puzuPWa3iSJgORKLahhAtp2qXczIu6xRFJMT97W96ScSKavaAFUwFjqkZuH13vgT_Eadz5pMb6yYTCEhSthmJl7tbIouzHC4crEZxa8CVldsQULra0/s1600-h/Lapis_3.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 94px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivjV9lKp-ORXOXFAM70n6kiWuZ5puzuPWa3iSJgORKLahhAtp2qXczIu6xRFJMT97W96ScSKavaAFUwFjqkZuH13vgT_Eadz5pMb6yYTCEhSthmJl7tbIouzHC4crEZxa8CVldsQULra0/s400/Lapis_3.bmp" alt="" id="BLOGGER_PHOTO_ID_5415061106447482226" border="0" /></a><br /><br /><br /><br /><br /><br />Next the user should remove the positions (digits) in the subject line.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeBu-YuHvhKeigcVAeP5XD1X4pTLR8sMRnwdMyyxIfXWktKL4f2VIwuQGJ1IoOmdnDQKRQUrwbgTzCVjx040texkUop_Fl5pH2Nu2boIKZ-ckJSZkkdV4BpD9OrAeuJGC-r9mS_rtwIaU/s1600-h/Lapis_4.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 199px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgeBu-YuHvhKeigcVAeP5XD1X4pTLR8sMRnwdMyyxIfXWktKL4f2VIwuQGJ1IoOmdnDQKRQUrwbgTzCVjx040texkUop_Fl5pH2Nu2boIKZ-ckJSZkkdV4BpD9OrAeuJGC-r9mS_rtwIaU/s400/Lapis_4.bmp" alt="" id="BLOGGER_PHOTO_ID_5415061654351903394" border="0" /></a><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />The screen shot below shows the highlighted digits to be omitted.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjU79KpKZGu1CtznycPMzXMj7A9w7DbS4eNEInW6rgumKA2Fz9DeHHCxdf1Nk8NAPQ4oMvFRSJDCQQv8iChphSk47uoTN-zIx4wWN6fPzPfy16_uFT5DsTlDyew-1Ljyxc-ei2cG4BrzQ0/s1600-h/Lapis_5.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 94px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjU79KpKZGu1CtznycPMzXMj7A9w7DbS4eNEInW6rgumKA2Fz9DeHHCxdf1Nk8NAPQ4oMvFRSJDCQQv8iChphSk47uoTN-zIx4wWN6fPzPfy16_uFT5DsTlDyew-1Ljyxc-ei2cG4BrzQ0/s400/Lapis_5.bmp" alt="" id="BLOGGER_PHOTO_ID_5415061811912784914" border="0" /></a><br /><br /><br /><br /><br /><br />The screen shot below shows the information after omitting the numbers from the subject line.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhj2UFyr3DdP3L3j0s_XMmiQg77w6eznpjBc6F6nJK_KBbZr4W3aP55Qd5aSNWPmb0lWHZR_IXD9PHslETSb_NkcC6Yn7heIrwR7zjYxBLxDNLHJ7R-zN0NY2l2Z7W3KWhYrOqSuDSqjig/s1600-h/Lapis_6.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 94px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhj2UFyr3DdP3L3j0s_XMmiQg77w6eznpjBc6F6nJK_KBbZr4W3aP55Qd5aSNWPmb0lWHZR_IXD9PHslETSb_NkcC6Yn7heIrwR7zjYxBLxDNLHJ7R-zN0NY2l2Z7W3KWhYrOqSuDSqjig/s400/Lapis_6.bmp" alt="" id="BLOGGER_PHOTO_ID_5415062044549920066" border="0" /></a><br /><br /><br /><br /><br /><br />Next the word “subj:” should be omitted also.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYLkAa908mRJjrCrCB2zQd_IKd7mxyNuBXfB2vDsQfy_i-PMl8O5E6oqq33U9tTHNT7iBq92vWQwOlj9ANoH9E-2iLLx6OHRJ8-q3LSm9nwyRr3wrP5uPqxwuFLeuF0G2YXarMVIo_pxo/s1600-h/Lapis_7.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 197px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYLkAa908mRJjrCrCB2zQd_IKd7mxyNuBXfB2vDsQfy_i-PMl8O5E6oqq33U9tTHNT7iBq92vWQwOlj9ANoH9E-2iLLx6OHRJ8-q3LSm9nwyRr3wrP5uPqxwuFLeuF0G2YXarMVIo_pxo/s400/Lapis_7.bmp" alt="" id="BLOGGER_PHOTO_ID_5415062614505782818" border="0" /></a><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4OoE1Z4GCYKwk0p9IGPbVPjymxiFhlxGRG2epxM83izpBL6pdXb0r-XA6HalbOLYsj14CH3iO3wdXHMiNSyxfEA4ivwa6o9X3bu6fo5bv1zqW2rNd5JPIgHNpH0hPKNpxKpS7uEkYrPw/s1600-h/Lapis_8.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 94px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi4OoE1Z4GCYKwk0p9IGPbVPjymxiFhlxGRG2epxM83izpBL6pdXb0r-XA6HalbOLYsj14CH3iO3wdXHMiNSyxfEA4ivwa6o9X3bu6fo5bv1zqW2rNd5JPIgHNpH0hPKNpxKpS7uEkYrPw/s400/Lapis_8.bmp" alt="" id="BLOGGER_PHOTO_ID_5415063632455449954" border="0" /></a><br /><br /><br /><br /><br /><br />The screen shot below shows the pattern to remove any extra spaces in the subject line. In case of any gaps (-), they should also be removed.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj39nkT-GyHvJVPfAtwixlx9Rb81XUGnP4yIqEBlpySBKdi6G06LC5h8-vYL_R-iTQ6qabHPgAlcphJoL0cDsvWkr-X7kT87sjkuhqh4Ng3VrhEKk5COwaSLnkfZ-h3eeFXCmbukSE9c3I/s1600-h/Lapis_9.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 196px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj39nkT-GyHvJVPfAtwixlx9Rb81XUGnP4yIqEBlpySBKdi6G06LC5h8-vYL_R-iTQ6qabHPgAlcphJoL0cDsvWkr-X7kT87sjkuhqh4Ng3VrhEKk5COwaSLnkfZ-h3eeFXCmbukSE9c3I/s400/Lapis_9.bmp" alt="" id="BLOGGER_PHOTO_ID_5415063848258783618" border="0" /></a><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7kJUj8BOffeGWCmYbE2eNdicsjNM10Hl9IXq0AsAzGe6dFMiHBoEJzuvrEK4RZdXYSU72y2jnYoeCQge0pynyzUqjrjAihdeyrEO5LqAyEpY8HO9iXV0igf-GWPfGdBzLoKir2nAv6uA/s1600-h/Lapis_10.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 95px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7kJUj8BOffeGWCmYbE2eNdicsjNM10Hl9IXq0AsAzGe6dFMiHBoEJzuvrEK4RZdXYSU72y2jnYoeCQge0pynyzUqjrjAihdeyrEO5LqAyEpY8HO9iXV0igf-GWPfGdBzLoKir2nAv6uA/s400/Lapis_10.bmp" alt="" id="BLOGGER_PHOTO_ID_5415064081797119570" border="0" /></a><br /><br /><br /><br /><br /><br /><br />The screen shot below shows the pattern to remove extra information from the header line.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTAP59Wiy90q1Dp3VjOh3uOFPy9j4jh1n6qFf233oR_byN-qCAyrZA4Lm3a-rSE1z75SUoDNYTq-krYFNjsWCN06RBm-1nHmdWV-k2MSvxboIBzoHSujPIQf2u-EAx1kefQ7wDq9U6EZc/s1600-h/Lapis_11.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 198px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTAP59Wiy90q1Dp3VjOh3uOFPy9j4jh1n6qFf233oR_byN-qCAyrZA4Lm3a-rSE1z75SUoDNYTq-krYFNjsWCN06RBm-1nHmdWV-k2MSvxboIBzoHSujPIQf2u-EAx1kefQ7wDq9U6EZc/s400/Lapis_11.bmp" alt="" id="BLOGGER_PHOTO_ID_5415064239848940034" border="0" /></a><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />The screen shot below shows the required output.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_sLHKKBgJXRA5B2otCzHqz-zB9_tu_TWUWYnJr_5ny6Nz2-DsWmrEFyyt5k8CBySOZM1zCOATgYa5ioRe2BQOBTpVOgk6pUroIgexyuZ7F8hEK6NV7SZ2_j1asnjVPt0S2jJ4RyGBBRk/s1600-h/Lapis_12.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 400px; height: 95px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_sLHKKBgJXRA5B2otCzHqz-zB9_tu_TWUWYnJr_5ny6Nz2-DsWmrEFyyt5k8CBySOZM1zCOATgYa5ioRe2BQOBTpVOgk6pUroIgexyuZ7F8hEK6NV7SZ2_j1asnjVPt0S2jJ4RyGBBRk/s400/Lapis_12.bmp" alt="" id="BLOGGER_PHOTO_ID_5415064418024160466" border="0" /></a>Pawanhttp://www.blogger.com/profile/10674070824859904556noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-85244953528531569402009-09-27T19:33:00.012+08:002009-11-01T15:37:27.113+08:0036) OpenBabel GUI - file format converter<span class="Apple-style-span" style="line-height: 16px;"><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;"><div style="text-align: center;"><span class="Apple-style-span" style="text-decoration: underline;"><b><br /></b></span></div><div><br /></div>It is a chemical toolbox designed to speak the many languages of chemical data.</span></span></span><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="line-height: 16px;font-size:medium;" ><br /></span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="line-height: 16px;">OpenBabel GUI for windows can be downloaded from the following website,</span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="line-height: 16px;"><br /></span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="line-height: 16px;"><a href="http://www.brothersoft.com/open-babel-download-208843.html">http://www.brothersoft.com/open-babel-download-208843.html</a>,</span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="line-height: 16px;"><br /></span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="line-height: 16px;">OpenBabel is also available for LINUX and MACINTOSH,</span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="line-height: 16px;"><br /></span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="line-height: 16px;font-size:medium;" ><h3><span class="Apple-style-span" style="font-size:medium;"><span class="Apple-style-span" style="color: rgb(0, 102, 0);"><span class="Apple-style-span" style="text-decoration: underline;">Basic operation:</span></span></span></h3> <p>OpenBabel converts chemical objects (currently molecules or reactions) from one file format to another. This interface is an alternative to a command line and has the same capabilities.</p> <p>- Select the type of the type of the input file from the dropdown list.</p> <p>- Click the "..." button and select the file. Its contents are displayed.</p> <p>- Choose the output format and file in a similar way. You can merely display the output without saving it by not selecting an output file or by checking "Output below only..".</p> <p>- Click the "Convert" button.</p> <p>The message window below the button gives the number of molecules converted, and the contents of the output file are displayed.</p> <p>By default, all the molecules in an input file are converted if the output format allows multiple molecules.</p></span></span></div><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj46S7rVyknIrYdaugm_knwZyoRDj5fbDeOFMxVCsIBKUJJPiPyO7qwn8N-QK6orwWPlor0D7UpRX60U8XfakNBugN1pzl_ZPuiO_EA0kWnhd6dj69VWyDivhBGT2D5aesw37GrsJSMULg/s1600-h/OBGUIScreenshot.png"></a><div><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj46S7rVyknIrYdaugm_knwZyoRDj5fbDeOFMxVCsIBKUJJPiPyO7qwn8N-QK6orwWPlor0D7UpRX60U8XfakNBugN1pzl_ZPuiO_EA0kWnhd6dj69VWyDivhBGT2D5aesw37GrsJSMULg/s1600-h/OBGUIScreenshot.png" style="text-decoration: none;"><img style="margin: 0px auto 10px; text-align: left; display: block; cursor: pointer; width: 320px; height: 202px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj46S7rVyknIrYdaugm_knwZyoRDj5fbDeOFMxVCsIBKUJJPiPyO7qwn8N-QK6orwWPlor0D7UpRX60U8XfakNBugN1pzl_ZPuiO_EA0kWnhd6dj69VWyDivhBGT2D5aesw37GrsJSMULg/s320/OBGUIScreenshot.png" alt="" id="BLOGGER_PHOTO_ID_5386110648986674546" border="0" /></a><span class="Apple-style-span" style="color: rgb(255, 0, 0);">NOTE: This would be useful for the people who are handling different docking softwares, because the file formats for each docking software will differ, based on the type of algorithm used and the development of the software.</span></div>Roopa kothapallihttp://www.blogger.com/profile/06488556369176096892noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-31917226777168756712009-09-26T23:28:00.010+08:002009-09-27T10:52:30.807+08:0035) Autodock 4.0 (Installation and working)<div><br /></div><span class="Apple-style-span" style=" ;font-family:'Times New Roman';"><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style=" ;font-size:medium;">Autodock 4.0 can be found from the following website,</span></span></pre></span><div><a href="http://mgltools.scripps.edu/downloads"><span class="Apple-style-span" style="font-size:medium;">http://mgltools.scripps.edu/downloads</span></a></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;"><a href="http://mgltools.scripps.edu/downloads"></a>download the software according to your computer appropriate operating system,</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">Installation:</span></div><div><span class="Apple-style-span" style="font-size:medium;">I.</span><span class="Apple-style-span" style="text-decoration: underline;"><span class="Apple-style-span" style="font-size:medium;">windows installation:</span></span></div><div><span class="Apple-style-span" style="font-size:medium;"> 1.Double click on to the MGLTools setup file. </span></div><div><span class="Apple-style-span" style="font-size:medium;"> 2.Click "Next"</span></div><div><span class="Apple-style-span" style="font-size:medium;"> 3.Accept the license agreement</span></div><div><span class="Apple-style-span" style="font-size:medium;">4. Select your favorite destination folder to install the files and click 'Next"</span></div><div><span class="Apple-style-span" style="font-size:medium;"> 5. wait for a while for the files to get installed</span></div><div><span class="Apple-style-span" style="font-size:medium;">6. click on to the "Non commercial-Install all these packages"</span></div><div><span class="Apple-style-span" style="font-size:medium;"> 7. click on to each package license</span></div><div><span class="Apple-style-span" style="font-size:medium;"> 8. click "continue" button below</span></div><div><span class="Apple-style-span" style="font-size:medium;">9. If you wish to launch shortcuts on your desktop , you can just click "finish"</span></div><div><span class="Apple-style-span" style="font-size:medium;">10. And there your are ---- you can start working.</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">II.</span><span class="Apple-style-span" style="text-decoration: underline;"><span class="Apple-style-span" style="font-size:medium;"> Linux installation:</span></span></div><div><span class="Apple-style-span" style="color:#FF0000;"><span class="Apple-style-span" style="font-size:medium;">NOTE: Autodock need to install from </span><span class="Apple-style-span" style="color:#000099;"><span class="Apple-style-span" style="font-size:medium;">/root/</span></span><span class="Apple-style-span" style="font-size:medium;">, it can be installed from the </span><span class="Apple-style-span" style="color:#000099;"><span class="Apple-style-span" style="font-size:medium;">/home/</span></span><span class="Apple-style-span" style="font-size:medium;"> directory itself.</span></span></div><div><span class="Apple-style-span" style="color:#FF0000;"><span class="Apple-style-span" style="font-size:medium;"><br /></span></span></div><div><span class="Apple-style-span" style="font-family:'Lucida Grande', Verdana, Lucida, Helvetica, Arial, sans-serif;"><span class="Apple-style-span" style="border-collapse: collapse; "><b><span class="Apple-style-span" style="font-family:Georgia, serif;"><span class="Apple-style-span" style="border-collapse: separate; font-weight: normal;"><div><span class="Apple-style-span" style="font-size:medium;">1. Download MGLTools-1.5.2-Linux-x86-Install grant execute permission and run the installer.</span></div><div><span class="Apple-style-span" style="font-size:medium;">To grant execute permission, type the following command at a command prompt: </span><span class="Apple-style-span" style="color:#000099;"><span class="Apple-style-span" style="font-size:medium;">chmod +x MGLTools-1.5.2-Linux-x86-Install .</span></span></div><div><span class="Apple-style-span" style="font-size:medium;">You can also use file manager to grant execute permission (right-click on the downloaded file and select Properties).</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">2) In the install wizard, click Next, select the destination and click Next again.</span></div><div><span class="Apple-style-span" style="font-size:medium;">The default destination is </span><span class="Apple-style-span" style="color:#000099;"><span class="Apple-style-span" style="font-size:medium;">/usr/local/MGLTools-1.5.2 for the root user and $HOME/MGLTools-1.5.2 for all others</span></span><span class="Apple-style-span" style="font-size:medium;">. </span></div><div><span class="Apple-style-span" style="font-size:medium;">Please wait a few moments until the "License Agreements for add-on packages" window appears.</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">3) Complete the "License Agreements for add-on packages" form.</span></div><div><span class="Apple-style-span" style="font-size:medium;">See Filling add-on packages license form for details.</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">4) Finally, click Finish to complete installation,</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">The README file contains detailed information on how to setup your environmental variables for command line usage. </span></div></span></span></b></span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="border-collapse: collapse; line-height: 18px; "><span class="Apple-style-span" style="font-size:medium;"><br /></span></span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="border-collapse: collapse; line-height: 18px;"><span class="Apple-style-span" style="font-size:medium;"><br /></span></span></span></div><div><span class="Apple-style-span" style="font-size:medium;">Meanwhile download the following as well, </span></div><div><a href="http://autodock.scripps.edu/downloads"><span class="Apple-style-span" style="font-size:medium;">http://autodock.scripps.edu/downloads</span></a></div><div><span class="Apple-style-span" style="font-size:medium;">click on the above link, </span></div><div><span class="Apple-style-span" style="font-size:medium;">you will pop up with an registration form, kindly fill with necessary details and download the files which will be compatible to your operating system that your using.</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">This will contain 2 executable files,</span></div><div><span class="Apple-style-span" style="font-size:medium;">1. autogrid</span></div><div><span class="Apple-style-span" style="font-size:medium;">2.autodock.</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="color:#FF0000;"><span class="Apple-style-span" style="font-size:medium;">NOTE: Make sure you install everything in the same destination folder including the 2 executable files</span></span></div><div><span class="Apple-style-span" style="color:#FF0000;"><span class="Apple-style-span" style="font-size:medium;"><br /></span></span></div><div><span class="Apple-style-span" style="font-size:medium;">How to work on Autodock 4.0?</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">Here we go..!!</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">Follow the below steps,</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /></span></div><div><span class="Apple-style-span" style="font-size:medium;">*double click on to this icon </span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgF-0K6-J0WzB1JOEsD36heB2Y1VsV_h4hvpXNpU-yrjsXv9Bwd1pYr_B6T-_EohGlygKkactOZkXilIVnK1QmnDRykie2Zhs6NC-e79mG6Mn4QXTIztyTwNuQtn6PwTSmDulqXPrAFBRo/s1600-h/iccon.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 45px; height: 45px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgF-0K6-J0WzB1JOEsD36heB2Y1VsV_h4hvpXNpU-yrjsXv9Bwd1pYr_B6T-_EohGlygKkactOZkXilIVnK1QmnDRykie2Zhs6NC-e79mG6Mn4QXTIztyTwNuQtn6PwTSmDulqXPrAFBRo/s320/iccon.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5385966015950991458" /></a><div><span class="Apple-style-span" style="font-size:medium;">Your workspace will look like this,</span></div><div><span class="Apple-style-span" style="font-size:medium;"><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGSzax4pYiFQj31wBLTRNv9V8VnEIseJNCzqEU6CtZwcjrstixY-5eHdcIcTIhaTd0DSJnFCNJvggs7NJ8FZ8MPyjy0dlPAuwueA0Us9LgzNnHOx86OBbc7dDxD78kMdmZiCHiMQcTFDA/s1600-h/autodock_workspace.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 306px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGSzax4pYiFQj31wBLTRNv9V8VnEIseJNCzqEU6CtZwcjrstixY-5eHdcIcTIhaTd0DSJnFCNJvggs7NJ8FZ8MPyjy0dlPAuwueA0Us9LgzNnHOx86OBbc7dDxD78kMdmZiCHiMQcTFDA/s320/autodock_workspace.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5385966134524472322" /></a>,<br /></span></div><div><span class="Apple-style-span" style="font-family:'Times New Roman';"><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Kindly use the pdb and ligand files which comes along with the installation of Autodock 4.0, will be present in (MGLTools/MGL ToolsPckgs/Pmv/doc). Use hsg1.pdb (protein) and ind.pdb (ligand)</span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><b><span class="Apple-style-span" style="color:#006600;"><span class="Apple-style-span" style="text-decoration: underline;"><span class="Apple-style-span" style="font-size:medium;">Protein Preparation: </span></span></span></b><span class="Apple-style-span" style="font-size:medium;"> </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">File - Read Molecule - Open the file.pdb. </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Select - Select from string - Type HOH* (to remove water molecules)</span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Edit - Add Polar only </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">File - write PDB save ur file in pdbfile.pdb extension just without changing the path. just click and remove HETATM Click sort nodes before saving <span class="Apple-style-span" style="color:#006600;"><b>.</b></span></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;color:#006600;"><b><span class="Apple-style-span" style="font-size:medium;"><br /></span></b></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><b><span class="Apple-style-span" style="color:#006600;"><span class="Apple-style-span" style="text-decoration: underline;"><span class="Apple-style-span" style="font-size:medium;">Ligand Preparation:</span></span></span></b><span class="Apple-style-span" style="text-decoration: underline;"><span class="Apple-style-span" style="font-size:medium;"> </span></span><span class="Apple-style-span" style="font-size:medium;"> </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Ligand - input open ur ligand.pdb - just note down the summary of the ligand. </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Torsion tree - choose root </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">again go to torsion tree - detect root </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">again go to torsion tree - show root expansion </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">again go to torsion tree - choose torsions just click ok </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">again go to torison tree - set number of torsions give the number of torisons that you get in the summary of the (TORSDOF) when u open the ligand. </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Output Save the ligand file in the same directory in ligandfile.pdbqt </span><b><span class="Apple-style-span" style="color:#006600;"><span class="Apple-style-span" style="font-size:medium;"> </span></span></b></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;color:#006600;"><b><span class="Apple-style-span" style="font-size:medium;"><br /></span></b></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><b><span class="Apple-style-span" style="color:#006600;"><span class="Apple-style-span" style="text-decoration: underline;"><span class="Apple-style-span" style="font-size:medium;">Grid preparation:</span></span></span></b><span class="Apple-style-span" style="font-size:medium;"> </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Select select from string just type your active site residues and then click ok </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Flexible residues - input macromolecule - choose macromolecule - click on your pdb from the panel displayed. </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Flexible residues - choose torsions from the currently selected residues - active site residues alone will be highlighted. </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Flexible residues - redisplay the macromolecule </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Flexible residues - save the files in both flexible as (pdbfile_flex.pdbqt) rigid as (pdbfile_rigid.pdbqt) .</span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Grid - macromolecule - open- just open ur pdb_rigid.pdbqt file, ignore the warnings, if you have any metal ions in your proteinn , just open ur grid file and u can find (0.00) for ur metal ions, just find the valency for them from net and type maunally ther and again save it.you use this now. (if you dont hav metal ions), just ignore the warnings. </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">set map types - choose ligand - click on ur ligand from the panel displayed output - save in .gpf edit gpf - dontt do anything just click ok for the time being </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Run - run autogrid just browse and locate ur autogrid.exe file , just browse and locate file .gpf (grid parameter file) and note that everything should be in the same directory, were you saved your pdb in protien preparation, dont change the path for your wish, just save were it is saving just put your autodock.exe and autogrid.exe in the same directory were ur files has been saved </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;"><br /></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><b><span class="Apple-style-span" style="color:#006600;"><span class="Apple-style-span" style="text-decoration: underline;"><span class="Apple-style-span" style="font-size:medium;">Docking:</span></span></span></b><span class="Apple-style-span" style="font-size:medium;"> </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Docking - Macromolecule - set rigid file name - just again open ur pdb_rigid.pdbqt file Ligand - choose ur ligand search parameters- just delete one zero from the 2500000 (just make it to 4 zeros), otherwise it wil take very long time. </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Docking parameters- default other option-autodock 4 parameters- default output - save in ligandfile.dpf </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Edit DPF - just leave and click ok </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">Run - run autock just browse and locate ur autodock.exe file just browse and locate file .dpf (dock parameter file) and then click ok.</span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;"><br /></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="text-decoration: underline;"><b><span class="Apple-style-span" style="color:#006600;"><span class="Apple-style-span" style="font-size: medium;">Analysing the results:</span></span></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;font-size:130%;color:#006600;"><span class="Apple-style-span" style=";font-size:16px;"><b style=""><span class="Apple-style-span" style="font-size: medium; "><span class="Apple-style-span" style="color:#000000;">open the widget "Analyse" and click open, locate the ligand.dlg file,</span></span></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size: medium;"><b>Next click on to Macromolecule found below Dockings, just click open, it will open by default, if you cannot able to view your protein properly, simply press "N" button from the keyboard.</b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;font-size:130%;color:#006600;"><span class="Apple-style-span" style=";font-size:16px;"><b style=""><span class="Apple-style-span" style="font-size: medium; "><span class="Apple-style-span" style="color:#000000;"><br /></span></span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-wv_zatjb0EBqIWZvJnSb2rl1hdTPqT0vKZSQsI5c13yb08SDG2f0VHGbD1jkP6H-pQuMyNowTHhhc7Xk4xPxdDUIW-_KYOC1dm4VR3hW86P_r2APohEm-DpntlLxl-1qsYld-3Xmilk/s1600-h/dock2.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 305px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-wv_zatjb0EBqIWZvJnSb2rl1hdTPqT0vKZSQsI5c13yb08SDG2f0VHGbD1jkP6H-pQuMyNowTHhhc7Xk4xPxdDUIW-_KYOC1dm4VR3hW86P_r2APohEm-DpntlLxl-1qsYld-3Xmilk/s320/dock2.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5385966245587002130" /></a><span class="Apple-style-span" style="color:#000000;"><span class="Apple-style-span" style="font-size: medium;"><br /></span></span></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;font-size:130%;color:#006600;"><span class="Apple-style-span" style=";font-size:16px;"><b style=""><span class="Apple-style-span" style="color:#000000;"><span class="Apple-style-span" style="font-size: medium;">To view your results click on to conformations -play,</span></span></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;font-size:130%;color:#006600;"><span class="Apple-style-span" style=";font-size:16px;"><b style=""><span class="Apple-style-span" style="color:#000000;"><span class="Apple-style-span" style="font-size: medium;"><br /></span></span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUSD6sjz26h7_wNIxglCEnVRFn23au42ZH3x6IRQZgYV7p1isfUmynVUip_10OiHvl0WdJphD8MTYAs_wGA3LrQXRAKXfebPpHVA3MHI5IScuS4B59X_D_2TCDmCGfrokiN8YLYmxCNKI/s1600-h/dock3.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 300px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUSD6sjz26h7_wNIxglCEnVRFn23au42ZH3x6IRQZgYV7p1isfUmynVUip_10OiHvl0WdJphD8MTYAs_wGA3LrQXRAKXfebPpHVA3MHI5IScuS4B59X_D_2TCDmCGfrokiN8YLYmxCNKI/s320/dock3.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5385966315722101074" /></a><span class="Apple-style-span" style="font-size: medium;"><span class="Apple-style-span" style="color:#000000;">It will open a widget shown in the picture.</span></span></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;font-size:130%;color:#006600;"><span class="Apple-style-span" style=";font-size:16px;"><b style=""><span class="Apple-style-span" style="color:#000000;"><span class="Apple-style-span" style="font-size: medium;"><br /></span></span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDhRgO5uP0XPGcpyqGXSzEBP02mo4B8Wjhy7r0oc_y5gtMG-_45b-nZJwNRJ4mHYYJSE5J85SMpsK9G5rp1q8o8e79ca4w3QNh2BoTtDfnpq6N5j9pzSVIgJxlwveCEAfusuqYrvmAR8w/s1600-h/dock-4.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 302px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDhRgO5uP0XPGcpyqGXSzEBP02mo4B8Wjhy7r0oc_y5gtMG-_45b-nZJwNRJ4mHYYJSE5J85SMpsK9G5rp1q8o8e79ca4w3QNh2BoTtDfnpq6N5j9pzSVIgJxlwveCEAfusuqYrvmAR8w/s320/dock-4.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5385966459948149106" /></a><br /></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;font-size:130%;color:#006600;"><span class="Apple-style-span" style=";font-size:16px;"><b style=""><span class="Apple-style-span" style="font-size: medium;"><span class="Apple-style-span" style="color:#000000;">click on to the ampersand (&) symbol.</span></span></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;font-size:130%;color:#006600;"><span class="Apple-style-span" style=";font-size:16px;"><b style=""><span class="Apple-style-span" style="color:#000000;"><span class="Apple-style-span" style="font-size: medium;"><br /></span></span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJiuuY8hyCXAb1RydTgBWKdZPR_xooF71_X4sxJyjyOpRUiCsWQFCGdPHCZXz8TdXcGZby7QO33vNaIIn4c1bWZw3EQL9617JiB_LhNokgg0g3s9YA48oSV4IPiKJwWhiW6Z8wZdjgky8/s1600-h/dock-5.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 254px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJiuuY8hyCXAb1RydTgBWKdZPR_xooF71_X4sxJyjyOpRUiCsWQFCGdPHCZXz8TdXcGZby7QO33vNaIIn4c1bWZw3EQL9617JiB_LhNokgg0g3s9YA48oSV4IPiKJwWhiW6Z8wZdjgky8/s320/dock-5.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5385966522198291762" /></a><span class="Apple-style-span" style="color:#000000;"><span class="Apple-style-span" style="font-size: medium;">Analyse your results..!!</span></span></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size: medium;"><b><br /></b></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="color:#FF0000;"><span class="Apple-style-span" style="font-size:medium;">NOTE: kindly save all your files in the same folder where you have been installed your MGLTools and executable files, if you want to run the programme from your favourite folder of your choice, make sure that you place just the executable files alone in the place were you have saved your all files that you have been used during the course of working on Autodock, because without these executable files the programme wont run properly. </span></span><span class="Apple-style-span" style="font-size:medium;"> </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;"><br /></span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:medium;">For more details regarding the algorithm,f orcefields and interpretation of the data kindly go through the Autodock manual which is available at below mentioned web site, </span></span></pre><pre style="word-wrap: break-word; white-space: pre-wrap; "><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style=" white-space: normal; font-family:'Times New Roman';"><a href="http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools"><span class="Apple-style-span" style="font-size:medium;">http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools</span></a></span></span></pre></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:small;"><br /></span></span></div><div><span class="Apple-style-span" style="font-family:georgia;"><span class="Apple-style-span" style="font-size:small;"> </span></span></div></span></div>Roopa kothapallihttp://www.blogger.com/profile/06488556369176096892noreply@blogger.com9tag:blogger.com,1999:blog-1737804828852994104.post-56729206921305308742009-09-26T23:16:00.001+08:002009-09-26T11:18:13.236+08:0034) How to set up web blast using BioSlaxAt this stage you should have the bioslax installed, if not please refer to<br /><br /><a href="http://bioinfotutlets.blogspot.com/2009/05/9-guide-to-using-bioslax.html">A guide to using BioSlax</a> and/or <a href="http://bioinfotutlets.blogspot.com/2009/05/17-installing-bioslax-as-full-linux.html">Installing BioSlax as a full linux system to your hard drive </a><br /><br /><br />1. First, get your sequence dataset ready in FASTA format<br /><br />2. Create a directory (for example: /root/Desktop/db) and save the FASTA file of interest to this newly created directory<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYgIyY1gC1tIPqxvxSOTbzn5vnq-I8oR4Fb5e0awZVMJ8rh4VOJYSfNrjnGHMDprOpw_n3c9MErUnOFqflYsAL3AHnZ9jMQM6enHwR3pxP4mLKb09NEakq0J1COAScCer0dql6yXPYWz9c/s1600-h/image002.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 277px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYgIyY1gC1tIPqxvxSOTbzn5vnq-I8oR4Fb5e0awZVMJ8rh4VOJYSfNrjnGHMDprOpw_n3c9MErUnOFqflYsAL3AHnZ9jMQM6enHwR3pxP4mLKb09NEakq0J1COAScCer0dql6yXPYWz9c/s400/image002.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342730541636089666" /></a><br /><br />3. Now convert the FASTA formatted sequences into a blastable format, to do this, use the program “formatdb” which available for download from NCBI at <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download"><span><span class="Apple-style-span" style="font-size:small;">http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download</span></span></a><br /><br />*For BioSlax user, you do not need to download formatdb for BioSlax because it comes preinstalled<br /><br />4. At console terminal, use this command to invoke Formatdb:<br />formatdb –i <inputfilename>-p <sequencetype?><br />Examples:<br />#formatdb –i ecoli.nt –p F<br />#formatdb -i swissprot -p T -o T<br /><br />–p => type of sequence file;<br />T(rue) => the fasta file contains protein sequences<br />F(alse) => the fasta file contains nucleotide sequences<br />-o T => create an index file so that it is faster to run BLAST (optional)<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimH0_Ut43SqtErmuJf7TbQZjI1y7Ylyx6h5T1_theoM3_BUZzEMV75Bu6-ioDS6xIw4-DPJOxxVERRTNZv2bUHDLwoWJufyvnNCizuNlPcw6Vw9xBQs4dr3SDasTvjuNOv0xj4YYTq-ADh/s1600-h/image004.jpg"><img style="cursor:pointer; cursor:hand;width: 381px; height: 250px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimH0_Ut43SqtErmuJf7TbQZjI1y7Ylyx6h5T1_theoM3_BUZzEMV75Bu6-ioDS6xIw4-DPJOxxVERRTNZv2bUHDLwoWJufyvnNCizuNlPcw6Vw9xBQs4dr3SDasTvjuNOv0xj4YYTq-ADh/s400/image004.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342730777623623090" /></a><br /><br />If the command is successful, a bunch of new files are created.<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkc_Jhan1zvoAgZ2WsLQs1CgI2sQsDK2s1A8sgiy5kGd5AhXhcTBo6odE-GIis4XqFfKwpcgpjB96pLPvvD-YEPaFwwTIq-7U4FIcUzRhsaZL9NlWuYIF_8MJDUlBrGjI9KyQVLVpunzv4/s1600-h/image006.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 235px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkc_Jhan1zvoAgZ2WsLQs1CgI2sQsDK2s1A8sgiy5kGd5AhXhcTBo6odE-GIis4XqFfKwpcgpjB96pLPvvD-YEPaFwwTIq-7U4FIcUzRhsaZL9NlWuYIF_8MJDUlBrGjI9KyQVLVpunzv4/s400/image006.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342730970327524722" /></a><br /><br />5. Now, go to K-menu => BioSLAX => Desktop Apps => BLAST DB setup<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYXOod_8LABOizubuaT7_4JSou6PZkO4hGuSmrzkLhU5H2BtaFJeoZvXfMxfeUd7rOW1o4aKN_G_yq144kkgGQfUqDB_bDcYxLjjFvC0A9Vvl9y5V39e_I2ozjIw213pziYElH4Y_Gr4EU/s1600-h/image008.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 272px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYXOod_8LABOizubuaT7_4JSou6PZkO4hGuSmrzkLhU5H2BtaFJeoZvXfMxfeUd7rOW1o4aKN_G_yq144kkgGQfUqDB_bDcYxLjjFvC0A9Vvl9y5V39e_I2ozjIw213pziYElH4Y_Gr4EU/s400/image008.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342731165208016962" /></a><br /><br />6. Fill up or browse the path of the directory containing the formatdb formatted sequence files (the directory you created at part 1) => click on “Set BLAST DB Now!” for Web Blast to do the necessary setup configurations<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8mMMxmlD1LFRDempLyCwUPLyKbbNeDiFcqVR-NAz8DianjW4KiD8F39Yp9fw9vw-s3WUXMByjLzcqaj9p6TXWteZKZPzYEIIglONj6CfiUmbQYR_qI73kpreXLwg1vrlF0VMpixdszGLm/s1600-h/image010.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 167px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8mMMxmlD1LFRDempLyCwUPLyKbbNeDiFcqVR-NAz8DianjW4KiD8F39Yp9fw9vw-s3WUXMByjLzcqaj9p6TXWteZKZPzYEIIglONj6CfiUmbQYR_qI73kpreXLwg1vrlF0VMpixdszGLm/s400/image010.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342731615427102466" /></a><br /><br />* Please note that the example “/root/Desktop/db” directory is fine if it is on a hard disk or a “configsave” has been done. If it's on a machine booted by LiveCD & no “configsave” is done, the files will be lost when the system is shutdown. Therefore, we recommend that user to create the database outside the virtual environment, i.e in a USB hdd or thumb drive.<br /><br />7. We are done, below are the results you will see:<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2GjwjmLgGvf6IVfZAFbxtmkC81QGggVcsNix9oCNXsH4wAaUWhDgPjHPtuTwFAkHOD0NbgkOEXLWDtB85-DemgqhrB7LKXKb1BljpfPs8pPL1fmKGA57u6my10IHnBnO6tHStrIL-OGG_/s1600-h/image012.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 201px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2GjwjmLgGvf6IVfZAFbxtmkC81QGggVcsNix9oCNXsH4wAaUWhDgPjHPtuTwFAkHOD0NbgkOEXLWDtB85-DemgqhrB7LKXKb1BljpfPs8pPL1fmKGA57u6my10IHnBnO6tHStrIL-OGG_/s400/image012.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342731814256272354" /></a><br /><br />BLAST result page<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxFj72gRvRH22rnLhHKnyqrP0LVuRMUDpSWPeEPbCyYvz7GyET_ZDqaTSbe-qDbJ8cBBQclTgEl7juR3H0SqQoUbdxKrlUG_o4fhVoaVOHE-xPpvn2N4PeQQ3l8XoRSV_M2nBHReAmL8F1/s1600-h/image014.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 239px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxFj72gRvRH22rnLhHKnyqrP0LVuRMUDpSWPeEPbCyYvz7GyET_ZDqaTSbe-qDbJ8cBBQclTgEl7juR3H0SqQoUbdxKrlUG_o4fhVoaVOHE-xPpvn2N4PeQQ3l8XoRSV_M2nBHReAmL8F1/s400/image014.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342731948743779730" /></a><br /><br />The location of your database after setting up BLAST Db: /usr/local/wwwblast-2.2.17/db<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhoS_YeP0Ranih0VAxwWpDA52kCWwNSYcaGBVtl-fvnUSUV3N0PMPxaHjUEquD8rmNvUSXX1cl-lvkwPWoI055hZeT7vjPjCiuentEGG37FQJjPlJctscc3-zUbvlx0DDsdCvrfZV2Lg6cz/s1600-h/image016.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 376px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhoS_YeP0Ranih0VAxwWpDA52kCWwNSYcaGBVtl-fvnUSUV3N0PMPxaHjUEquD8rmNvUSXX1cl-lvkwPWoI055hZeT7vjPjCiuentEGG37FQJjPlJctscc3-zUbvlx0DDsdCvrfZV2Lg6cz/s400/image016.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342732129505141282" /></a><br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKpTQdQQwBtBfy2EX2fuOefdseKFDeK3p0qDhJYyNlra-B39mo4gWOIQGHxrYcm-tP3L5_-W1_khyphenhyphenelPSEnP9oUnP94VYoGL2oehQ94QSpJ_YUx9upwRLGz_yMvMcD7yP-d90_AbURp7hG/s1600-h/image018.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 322px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKpTQdQQwBtBfy2EX2fuOefdseKFDeK3p0qDhJYyNlra-B39mo4gWOIQGHxrYcm-tP3L5_-W1_khyphenhyphenelPSEnP9oUnP94VYoGL2oehQ94QSpJ_YUx9upwRLGz_yMvMcD7yP-d90_AbURp7hG/s400/image018.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5342732344304493202" /></a><br /><br /><br /></sequencetype?></inputfilename>cbeehttp://www.blogger.com/profile/13749285444941751919noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-52899088637921403942009-09-26T23:16:00.000+08:002009-09-26T11:13:17.679+08:0033) How to set-up the bioslax laptop serversAt this step you should have the bioslax installed in your laptop, if not please refer to<br /><a href="http://bioinfotutlets.blogspot.com/2009/05/9-guide-to-using-bioslax.html">A guide to using BioSlax</a> and/or <a href="http://bioinfotutlets.blogspot.com/2009/05/17-installing-bioslax-as-full-linux.html">Installing BioSlax as a full linux system to your hard drive </a><br /><br /><div><br />1. First of all, you need to change the password:<br /><ol><br /><li type="a"> Run the Konsole terminal<br /></li><li type="a"> <span style="color:red;">bioslax#: </span><span style="color:blue;"> passwd</span><br /></li><li type="a"> follow the instructions on the screen (please don’t set simple password)<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJ-NAZ-cR1Kqj1hf22iQWRWNRIKeM5cfS61aGzXgABHeFy7nyBVHVyNT-70BZvX3WfQ0KRdz7BXMpibckIdmByiHZiI8JloichZFN4Xqh76VmaF0evOerKiQLG_1ywLjUscUu_6jZtvZ7p/s1600-h/image002.jpg"><img style="cursor:pointer; cursor:hand;width: 400px; height: 147px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJ-NAZ-cR1Kqj1hf22iQWRWNRIKeM5cfS61aGzXgABHeFy7nyBVHVyNT-70BZvX3WfQ0KRdz7BXMpibckIdmByiHZiI8JloichZFN4Xqh76VmaF0evOerKiQLG_1ywLjUscUu_6jZtvZ7p/s400/image002.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5345356139813031762" /></a><br /></li></ol><br />2. To change host name: (skip this step if it has already been done)<br /><ol><br /><li type="a"> Run the Konsole terminal<br /></li><li type="a"> <span style="color:red;">root@slax: </span><span style="color:blue;">pico /etc/HOSTNAME</span><br /></li><li type="a"> Change “bioslax.maxonline.com.sg” to your host+domain name (e.g.group01.bic.nus.edu.sg).<br /></li><li type="a"> Reboot<br /></li></ol><br />3. If the previous step 2 did not work, do the following, otherwise skip to step 4:<br /><ol><br /><li type="a"> Run the Konsole terminal<br /></li><li type="a"> <span style="color:red;">bioslax#: </span><span style="color:blue;">cd /etc/rc.d</span><br /></li><li type="a"> <span style="color:red;">bioslax#: </span><span style="color:blue;">pico rc.M </span><br /></li><li type="a"> You will be in the file rc.M. Type ctrl-W to search for "HOSTNAME". Type ctrl-W again, press enter and it will search the next word containing "HOSTNAME". You should be looking for the line "Set hostname by using DHCP response".<br /></li><li type="a"> Comment the whole paragraph from "set hostname by using DHCP response" to "done" by typing # at the start of each line.<br /></li><li type="a"> Save the changes by typing ctrl-X.<br /></li><li type="a"> Run the Konsole terminal again.<br /></li><li type="a"> <span style="color:red;">bioslax#: </span><span style="color:blue;">netconfig</span><br /></li><li type="a"> There will be a blue window opened where you can enter the hostname, e.g."group01".<br /></li><li type="a"> Enter the domain name, e.g."bic.nus.edu.sg".<br /></li><li type="a"> Select "DHCP" as the network connection.<br /></li><li type="a"> At the "Set DHCP Hostname" window, leave it blank and press OK.<br /></li><li type="a"> Confirm the changes.<br /></li><li type="a"> Reboot<br /></li></ol><br />4. Set password for MYSQL<br /><ol><br /><li type="a"> Log in to Webmin (e.g. type http://group01.bic.nus.edu.sg:10000 for remote access) in Mozilla Firefox.<br /></li><li type="a"> Go to Servers<br /></li><li type="a"> Select MySQL Database Server<br /></li><li type="a"> Go to User Permissions<br /></li><li type="a"> Search for the row containing user “Anonymous”, host “localhost” and click on the "Anonymous" link to change the settings for that row:<br />Under “Permissions” Click “Select Table Data” (it will become highlighted) Click “Save”<br /></li><li type="a"> Search for the row containing user “Anonymous”, host “bioslax” and click on the "Anonymous" link to change the settings for that row:<br />Under “Hosts” click the radio button next to the text-box and in the textbox type in “groupXX”<br />Under “Permissions” Click “Select Table Data” (it will become highlighted)<br /> Click “Save”<br /></li><li type="a"> Search for the row containing user “root”, host “localhost” and click on the "Anonymous" link to change the settings for that row:<br />Under “Password” click the radio button for “Set to” and fill in the root password in the text box<br /> Click “Save”<br /></li><li type="a"> Search for the row containing user “root”, host “bioslax” and click on the "Anonymous" link to change the settings for that row:<br />Under “Password” click the radio button for “Set to” and fill in the root password in the text box<br />Under “Hosts” click the radio button next to the text-box and in the textbox type in “groupXX”<br />Click “Save”<br /><br /></li></ol><br />5. Three different ways to access the server remotely<br /><ol><br /><li type="a"> WinSCP (Freeware; <a href="http://winscp.net/">http://winscp.net/</a>).<br /><ol><br /><li type="i"> Hostname: group02.bic.nus.edu.sg<br /></li><li type="i"> Port number: 22<br /></li><li type="i"> Username: root (or any other username that you may have created on the server)<br /></li><li type="i"> Password: (type your password)<br /></li><li type="i"> Protocol: SFTP (allow SCP fallback)<br /></li><li type="i"> Click “Login”. If prompted for security alert, click “Yes”.<br /></li></ol><br /></li><li type="a"> Putty (Freeware; <a href="http://www.putty.nl/">http://www.putty.nl/</a>).<br /><ol><br /><li type="i"> Hostname: group02.bic.nus.edu.sg<br /></li><li type="i"> Port number: 22<br /></li><li type="i"> Connection type: SSH<br /></li><li type="i"> Click “Open”. If prompted for security alert, click “Yes”.<br /></li><li type="i"> Login as: root (or any other user id)<br /></li><li type="i"> Password: (type your password)<br /></li></ol><br /></li><li type="a"> Web browser (URL:<a href="http://group02.bic.nus.edu.sg/">http://group02.bic.nus.edu.sg</a>)<br /><ol><br /><li type="i"> To access files from the web, you should save your web pages in the “/var/www/htdocs” folder<br /></li><li type="i"> To access pre-installed programs in Bioslax, such as blast and clustalw:<br /><ol><br /><li> <a href="http://group01.bic.nus.edu.sg/blast/">http://group01.bic.nus.edu.sg/blast/</a><br /></li><li> <a href="http://group01.bic.nus.edu.sg/clustalw/">http://group01.bic.nus.edu.sg/clustalw/</a><br /></li><li> <a href="http://group01.bic.nus.edu.sg/webphylip/">http://group01.bic.nus.edu.sg/webphylip/</a><br /></li><li> <a href="http://group01.bic.nus.edu.sg/t_coffee/">http://group01.bic.nus.edu.sg/t_coffee/</a><br /></li><li> <a href="http://group01.bic.nus.edu.sg/wemboss/">http://group01.bic.nus.edu.sg/wemboss/</a><br /></li><li> <a href="http://group01.bic.nus.edu.sg/sms2/">http://group01.bic.nus.edu.sg/sms2/</a></li></ol></li></ol></li></ol></div>cbeehttp://www.blogger.com/profile/13749285444941751919noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-77778308699759193512009-08-20T16:17:00.014+08:002009-08-25T11:19:03.073+08:0031) Multiple sequence titles in the same BLAST hitWe were curious about what it means when BLAST returns a BLAST hit indicated by a “>” but followed by multiple entries with different accession numbers.<br /><br />Are these sequences the same? And are they the same only at the aligned region or in the rest of the sequence as well?<br /><br />I did a check on how these sequences are related. Based on several examples (two listed below), for now, it could be concluded that these <span style="font-weight: bold; font-style: italic;">entries that fall under the same BLAST hit are full sequence duplicates</span>. However, in terms of annotations they could be from different isolates.<br /><br /><span style="font-weight: bold;">Case 1: 2 accession numbers under the same BLAST hit</span><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFVi_1wnjkVVxc9eMhNPyDnzCldnEaywtUBtclV3zR9goBK-4A57So_DmJS64f7AwUJzGuZZyYir9RDOPsFUPu0m-B5XJemTLlsy4Kz_Ip2Qe2zN5dNkxzjX6ZS56t9yjVIgiBQ6buDxM/s1600-h/31_1.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 563px; height: 260px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFVi_1wnjkVVxc9eMhNPyDnzCldnEaywtUBtclV3zR9goBK-4A57So_DmJS64f7AwUJzGuZZyYir9RDOPsFUPu0m-B5XJemTLlsy4Kz_Ip2Qe2zN5dNkxzjX6ZS56t9yjVIgiBQ6buDxM/s400/31_1.png" alt="" id="BLOGGER_PHOTO_ID_5371961010708717698" border="0" /></a>Alignment between full sequences of Q6R325.1 and AAS01728.1<br /><ul><li>100% identity, i.e. full sequences are exactly the same</li><li>Same author</li><li>Swissprot entry (Q6R325.1) has cross-reference to Genbank entry (AAS01728.1)</li></ul><span style="font-weight: bold;">Case 2: Multiple accession numbers under the same BLAST hit</span><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuoFuYDaJVp7y08LSnsag_nd8GysgNeyRqx2LPDJC-eQz_17qHdbTQ9hV5rlJyhpHywYSfjjrjx9WUAFppP9_8HifXzgYBpfly_3Ye18X3QQG6ki3NjAHL_Pb1u5IQ80g20bq-WVAygkk/s1600-h/31_2.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 527px; height: 277px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuoFuYDaJVp7y08LSnsag_nd8GysgNeyRqx2LPDJC-eQz_17qHdbTQ9hV5rlJyhpHywYSfjjrjx9WUAFppP9_8HifXzgYBpfly_3Ye18X3QQG6ki3NjAHL_Pb1u5IQ80g20bq-WVAygkk/s400/31_2.png" alt="" id="BLOGGER_PHOTO_ID_5371961299208830130" border="0" /></a>Multiple alignment of full sequences of all sequence titles<br /><ul><li>Perfect alignment</li><li>Same author</li><li>Only the isolate annotation is different</li></ul>Nataschahttp://www.blogger.com/profile/00488343928977099325noreply@blogger.com3tag:blogger.com,1999:blog-1737804828852994104.post-37278713647765834332009-08-19T13:20:00.011+08:002009-08-19T13:43:18.376+08:0030) Using VLOOKUP (or HLOOKUP) in Microsoft ExcelVLOOKUP is a very useful formula in Excel to perform tasks such as:<br /><ul><li>Data comparions between sheets</li><li>Checking for discrepancies</li><li>Linking data between sheets</li></ul>and the list can go on!<br /><br />The formula looks like this:<br />VLOOKUP(lookup_value,table_array,col_index_num,range_lookup)<br /><br />--<br /><span style="font-weight: bold; font-style: italic;">lookup_value</span>: The value to search in the first column of the table array<br /><br /><span style="font-weight: bold; font-style: italic;">table_array</span>: Two or more columns of data. The values in the first column of table_array are the values searched by lookup_value. These values can be text, numbers, or logical values. Uppercase and lowercase text is equivalent.<br /><br /><span style="font-weight: bold; font-style: italic;">col_index_num</span>: The column number in table_array from which the matching value must be returned. A col_index_num of 1 returns the value in the first column in table_array; a col_index_num of 2 returns the value in the second column in table_array, and so on. If col_index_num is:<br /><ul><li>Less than 1, VLOOKUP returns the #VALUE! error value.</li><li>Greater than the number of columns in table_array, VLOOKUP returns the #REF! error value.</li></ul><br /><span style="font-weight: bold; font-style: italic;">range_lookup</span>: A logical value that specifies whether you want VLOOKUP to find an exact match or an approximate match:<br /><ul><li>If FALSE, VLOOKUP will only find an exact match. In this case, the values in the first column of table_array do not need to be sorted. If there are two or more values in the first column of table_array that match the lookup_value, the first value found is used. If an exact match is not found, the error value #N/A is returned.</li></ul><ul><li>If TRUE or omitted, an exact or approximate match is returned. If an exact match is not found, the next largest value that is less than lookup_value is returned. </li></ul>--<br /><br />The values in the first column of table_array must be placed in ascending sort order; otherwise, VLOOKUP may not give the correct value. You can put the values in ascending order by choosing the Sort command from the Data menu and selecting Ascending. For more information, see Default sort orders.<br /><br />A good reference for more details of the formula can be found <a href="http://office.microsoft.com/en-us/excel/HP052093351033.aspx">here</a>.<br />These details are illustrated in the following example.<br /><br /><span style="font-weight: bold;">Step 1: </span><br /><span style="font-weight: bold;">a)</span> Once you have your table_array (i.e. your “reference dataset” with the first column containing), and the list which you would like to lookup for, enter the VLOOKUP formula in the cell as follows:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhpPdv-0J1jepeBMvq6D12Wk_6fvwV3hYFXCEZ461CSocEmPRht1r6wWPXSW4FTrYNI6KtUsP2Iw8hXQu0hMh7QMVGbhCZVPB2tEfFhJUY3nKY9o1lmomOsF2QFt8ZJklc9f7ETIYrNVRI/s1600-h/30_1.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 99px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhpPdv-0J1jepeBMvq6D12Wk_6fvwV3hYFXCEZ461CSocEmPRht1r6wWPXSW4FTrYNI6KtUsP2Iw8hXQu0hMh7QMVGbhCZVPB2tEfFhJUY3nKY9o1lmomOsF2QFt8ZJklc9f7ETIYrNVRI/s400/30_1.png" alt="" id="BLOGGER_PHOTO_ID_5371541813873513938" border="0" /></a><br /><span style="font-weight: bold;">b)</span> Note that in the formula, I have put in a “$” sign for the data source table indexes. This is to lock the table_array as A2:B5 and not allow it to slide as we drag the formula down to the rest of the cells.<br />This is what it’ll look like if I had not put the “$” sign there:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOq4HP0xJudNFLM1R5vRKzI0sIVSZyV2NCIYmxPc4q6MFNgIAKRGCI0L-TZkq7nUbpub6KxuPmC9D9gbmA-GMkwakwB9FqDCEtYoc6cftzdpFAMWbM0OJeZ5ymZfIW84ybdjcwJ-eRuDE/s1600-h/30_2.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 123px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOq4HP0xJudNFLM1R5vRKzI0sIVSZyV2NCIYmxPc4q6MFNgIAKRGCI0L-TZkq7nUbpub6KxuPmC9D9gbmA-GMkwakwB9FqDCEtYoc6cftzdpFAMWbM0OJeZ5ymZfIW84ybdjcwJ-eRuDE/s400/30_2.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5371542060737400066" /></a><br />Notice that the data source table_array indexes have shifted (green box) and hence the value “1” could not be found. This will result in a #N/A error, as follows:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiryHntCefjhNPodpqdmJ9dwluGyIv-EzYGkb1BuZTAds2Hr1eTDpjiaJW7QbyO1JBiEksEN7jQxkjiUE-OJikdKE0NgMjeptC5pqrg7tsvlDn67e0qHo22Jn5Erz5h4CSV7ncnGptTLUw/s1600-h/30_3.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 157px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiryHntCefjhNPodpqdmJ9dwluGyIv-EzYGkb1BuZTAds2Hr1eTDpjiaJW7QbyO1JBiEksEN7jQxkjiUE-OJikdKE0NgMjeptC5pqrg7tsvlDn67e0qHo22Jn5Erz5h4CSV7ncnGptTLUw/s400/30_3.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5371542230152440978" /></a><br />To avoid this, it is safer to use the “$” sign in your formula as shown in the Step 1(a).<br /><br /><span style="font-weight: bold;">Step 2</span>: Hover on the edge of the cell, till your cursor becomes a “+”.<br />Click and drag the formula down to fill the rest of the cells.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcbN7A-u4f40oMamvLHupj2BJuM6xQ1Zw7Q-QvR6vEaVonN-TyK-zSGN6i0Gsn9xoR1cFmDYYpcfuilv8Aw_nWtYtqYQ5aVz7bX-81uBxQd6EVrNo-Y-nkISamuKPE6j96QiqQ-_UzBEo/s1600-h/30_4.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 158px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcbN7A-u4f40oMamvLHupj2BJuM6xQ1Zw7Q-QvR6vEaVonN-TyK-zSGN6i0Gsn9xoR1cFmDYYpcfuilv8Aw_nWtYtqYQ5aVz7bX-81uBxQd6EVrNo-Y-nkISamuKPE6j96QiqQ-_UzBEo/s400/30_4.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5371542568273858658" /></a><br /><br /><span style="font-weight: bold;">Step 3</span>: And this is what you’ll get:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZgjmjRDVG809pxdLNmAivx8VIUZXfosm83iIS-az-P0pVms2A1wDGQonPCQD8b_CQdtmrM5uftz4uaevnJCxMFNnSmcZXWpyvW0Ge7RovYrQw9nDaOkMJdh5LiOTgV7jv6_jF6kb_DUE/s1600-h/30_5.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 147px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZgjmjRDVG809pxdLNmAivx8VIUZXfosm83iIS-az-P0pVms2A1wDGQonPCQD8b_CQdtmrM5uftz4uaevnJCxMFNnSmcZXWpyvW0Ge7RovYrQw9nDaOkMJdh5LiOTgV7jv6_jF6kb_DUE/s400/30_5.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5371542762607061298" /></a><br /><span style="font-weight: bold;">For data comparions from different sheets:</span><br />If your source/reference data is stored in another sheet, simply add the sheet name at the beginning of the [table_array] field, like this:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiujpx9Il4gMQYCxU8S2Ou6uRLbvzwHTRMHZ2FxhKPW7LMkkblFw_rkFVv-1r2EH0dwjLorVD0VFi8tOozjQGkt0E8adJfrhfM6HggCn2YqQ3-6_upJbxagUEQC6MymmTdKmsSoTEVIy4/s1600-h/30_6.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 130px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiujpx9Il4gMQYCxU8S2Ou6uRLbvzwHTRMHZ2FxhKPW7LMkkblFw_rkFVv-1r2EH0dwjLorVD0VFi8tOozjQGkt0E8adJfrhfM6HggCn2YqQ3-6_upJbxagUEQC6MymmTdKmsSoTEVIy4/s400/30_6.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5371542931586911522" /></a><br /><span style="font-weight: bold;">What if I have a horizontal set of data as my table_array?</span><br />The VLOOKUP formula described above is used when the table_array is vertical and the lookup values are in the first column.<br />Use HLOOKUP when the table_array is horizontal and the lookup values are in the top row. The other details, such as using the “$” sign, remain the same.<br /><br /><span style="font-weight: bold;">What does #N/A mean?</span><br />The error #N/A indicates that the source for a particular data was not found in the table_array. This could mean either (i) your table_array had shifted, as explained above in Step 1(b) or (ii) the data of interest is not present in the reference table.<br /><br /><span style="font-weight: bold;">Counting the #N/A's</span><br />Sometimes we might be interested in the number of data entries that do not have a match in the table_array (the reference table).<br /><br />To count the number of #N/A errors in a dataset, use this formula:<br /><br />=IF(ISNA(A1),1,0)<br /><br />This prints 1 if cell "A1" contains #N/A, else prints 0. Sum up the column to obtain a total.Nataschahttp://www.blogger.com/profile/00488343928977099325noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-77627871009502040362009-08-19T12:35:00.013+08:002009-08-19T13:12:08.980+08:0029) Removing sequences that are fully gapped from alignment using BioEditLet’s say you have an alignment that looks like this after you cleaved out a particular region from a longer protein:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEggQwPvWM-V5eeNPzIvtTQEl0m0uaZRArSrG6jQ3uL3cF_R97E2yBuuYrrYtU0FXIUp7Vwzvg2G-WYXGkv81vo5ogwFAQSHK5P1Q4uqk43AgXuiwlt1Of5SbUyzVKD5ggqLM1UKS3ioJgM/s1600-h/vlookup_1.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 344px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEggQwPvWM-V5eeNPzIvtTQEl0m0uaZRArSrG6jQ3uL3cF_R97E2yBuuYrrYtU0FXIUp7Vwzvg2G-WYXGkv81vo5ogwFAQSHK5P1Q4uqk43AgXuiwlt1Of5SbUyzVKD5ggqLM1UKS3ioJgM/s400/vlookup_1.png" alt="" id="BLOGGER_PHOTO_ID_5371530207501951186" border="0" /></a>We intend to remove sequences that are fully gapped, as shown in red box above.<br /><br />To do this,<br /><ol><li>Click on: Sequence >> Filter out sequences containing certain characters >> Cut them to new alignment<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikC2fs7J6YoD-zbTNSnmUJXBPFW7Nyz2Rmz1l76Rf7hKP6Vky5A1v3ZiSpFHzh9SyTWl6CGRx4VW6qqM0aSiV-rsGSkx28f36o9KDsHtFSbU3ZKrgpcXDwYFEPh9McMmZ41iVWUBZ8jLo/s1600-h/vlookup_2.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 122px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikC2fs7J6YoD-zbTNSnmUJXBPFW7Nyz2Rmz1l76Rf7hKP6Vky5A1v3ZiSpFHzh9SyTWl6CGRx4VW6qqM0aSiV-rsGSkx28f36o9KDsHtFSbU3ZKrgpcXDwYFEPh9McMmZ41iVWUBZ8jLo/s400/vlookup_2.png" alt="" id="BLOGGER_PHOTO_ID_5371530383620075474" border="0" /></a></li><br /><li>Select <i style=""><u>Contain non-</u></i> and type “-“ in the textbox.<br />This means we are asking the tool to extract any sequence that contains a non-gap character.<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6dzfgmGXEFW0YwJL1gj1ecx3tw5QIiNXX5w3-0baUtKSmxWV8JSXRqqNC2FzuLhrpdkKGzoouM5iB5chkG9A1j9DZE2Nobrdh0ywJQ1xFsYdR-YLZc2cr-S9Nf1YCnOyGQRHt8CI6SHI/s1600-h/vlookup_3.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 160px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6dzfgmGXEFW0YwJL1gj1ecx3tw5QIiNXX5w3-0baUtKSmxWV8JSXRqqNC2FzuLhrpdkKGzoouM5iB5chkG9A1j9DZE2Nobrdh0ywJQ1xFsYdR-YLZc2cr-S9Nf1YCnOyGQRHt8CI6SHI/s400/vlookup_3.png" alt="" id="BLOGGER_PHOTO_ID_5371531024116007842" border="0" /></a></li><br />The sequences that are not fully gapped will be extracted to a new alignment, preserving the order of the sequences in the original alignment.<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQNAINi5Xj9CfaO_b6LlpA5UooskCisyv2AtMsmR-enufy7Nv1jL_pHOLJ0HnxOpm_FlNU3uTxHnCjWhznEDOPRL-cjPL-c2wNRq1UakT53uZDPeeNlNbA7NFldlozAfFGF8cQoBSc1tc/s1600-h/vlookup_4.png"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 345px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQNAINi5Xj9CfaO_b6LlpA5UooskCisyv2AtMsmR-enufy7Nv1jL_pHOLJ0HnxOpm_FlNU3uTxHnCjWhznEDOPRL-cjPL-c2wNRq1UakT53uZDPeeNlNbA7NFldlozAfFGF8cQoBSc1tc/s400/vlookup_4.png" alt="" id="BLOGGER_PHOTO_ID_5371531344121861250" border="0" /></a><br /><li>Save the output as a new .aln file, and you’ll have an alignment file without the fully gapped sequences!</li></ol>Nataschahttp://www.blogger.com/profile/00488343928977099325noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-55787165048304188792009-07-29T13:07:00.005+08:002009-07-29T13:43:58.405+08:0028) How to import tab delimited data into a table of a mySQL database in proline server???Steps to import a tab delimited data:<br /><br />1) Prepare your tab delimited data. Make sure that there are no headers included on the first line. File transfer in the data to proline either by WinSCP or SSH.<br /><br />2) Create a table in the mySQL database in proline. Make sure that the imported data would match to the column headers that you have defined in the table respectively.<br /><br />For example, "D1_00001" in my data would match to "Accession" column that I have defined in my SQL table.<br /><br /><br />3) Login to proline and SQL. (refer to previous posts 2 and 23)<br /><br />4) Use the following SQL command:<br /><br />LOAD DATA LOCAL INFILE 'file_with_full_pathname' INTO TABLE <span style="font-style:italic;">name_of_table</span><br /><br />For example:<br /><br />mysql> \g LOAD DATA LOCAL INFILE '/projects/denvdb/www/DENV.txt' INTO TABLE DENV<br /><br /><br />It will work even though I did not specify that the data is tab separated.<br /><br />Please refer <a href="http://dev.mysql.com/doc/refman/6.0/en/loading-tables.html">here</a> for more information.<br /><br />For comma delimited data, the sql command is the same except that you may need to add in FIELDS TERMINATED BY ','<br /><br />However I have not tested this out yet.^BeNBeN^http://www.blogger.com/profile/11629878814774576609noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-13249865472276665802009-06-10T17:15:00.006+08:002009-06-10T17:32:54.279+08:0027) How to create a metadata file for AVANA???In order to do mutual information analysis (e.g in post 25), we need to create a metadata file:<br /><br />a) Create a blank excel sheet.<br /><br />b) Paste your GI numbers correspondingly to the first column of the sheet.<br /><br />c) In the second column, insert the serotype matching with the corresponding gi numbers.<br /><br />d) In the third column, insert the protein name matching with the corresponding gi numbers.<br /><br />e) Make sure that you include headers in the first row or AVANA will treat the first data as a header, thus missing out 1 data in your analysis.<br /><br />f) Once all the data is in, save the spreadsheet as a comma-separated file by changing "Save as type" to "CSV (Comma delimited)".<br /><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEir4IzXwYKcPksNl2ucJ4toyBrxQjFCR4jW2Ys97bofPzBoej9600-Ycz4xXgeBKP74s6hSotOWIPJOYBSrc8t9ymMrWth1U4wiUsrEZkd4jVw2gvV0M9NwjKP52PsCmeKY_ZQJK6OGWGzx/s1600-h/metadata2.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 321px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEir4IzXwYKcPksNl2ucJ4toyBrxQjFCR4jW2Ys97bofPzBoej9600-Ycz4xXgeBKP74s6hSotOWIPJOYBSrc8t9ymMrWth1U4wiUsrEZkd4jVw2gvV0M9NwjKP52PsCmeKY_ZQJK6OGWGzx/s400/metadata2.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345628559686905954" /></a><br /><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjegIEPQohMrqla7VKXIK43BWFGoPKcSrJ8VHMfFdMrAQhwMQEfGUAcZSsooZW3AwHPMBxk7R_IQMuKagBdfiAh0-8mfrPpChXF7LyW6cYixFPEiEVCZVqi9JKwhngm-_YbPueKuS8C_cAE/s1600-h/metadata1.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 301px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjegIEPQohMrqla7VKXIK43BWFGoPKcSrJ8VHMfFdMrAQhwMQEfGUAcZSsooZW3AwHPMBxk7R_IQMuKagBdfiAh0-8mfrPpChXF7LyW6cYixFPEiEVCZVqi9JKwhngm-_YbPueKuS8C_cAE/s400/metadata1.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345627382644615330" /></a><br /><br />This is a sample metadata of my dengue virus records with capsid protein entries for all serotypes, which i named as "All_C.csv". The pictures show the start and the end of the sheet respectively.^BeNBeN^http://www.blogger.com/profile/11629878814774576609noreply@blogger.com2tag:blogger.com,1999:blog-1737804828852994104.post-72278508678991194682009-06-05T16:54:00.003+08:002009-06-10T16:59:39.613+08:0025) Steps for obtaining mutual information between two sequence alignments in AVANA:Steps for obtaining mutual information between two sequence alignments in AVANA: (e.g comparing D1_C to D2_C,D3_C,D4_C):<br /><br /><br />1) Load your taln file (e.g. All_C.taln) in AVANA<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMZCUM_30MkHL1NBw50ktDxBSiAg9UEDHfHWbeHvdeBg5SXmt5Juk9R3tqCLEBmDlFaRvnmjbM7Lan13sGz_WjW7rI46bWcI04er73EF76X0aIz4vfxLyS7-zSqJNd6nSFRSYADadviZYD/s1600-h/AVANA1.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 264px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMZCUM_30MkHL1NBw50ktDxBSiAg9UEDHfHWbeHvdeBg5SXmt5Juk9R3tqCLEBmDlFaRvnmjbM7Lan13sGz_WjW7rI46bWcI04er73EF76X0aIz4vfxLyS7-zSqJNd6nSFRSYADadviZYD/s400/AVANA1.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345266096195978082" /></a><br /><br /><br />2) Load your metadata (e.g. All_C.csv) in AVANA<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEJwAj1srpG_VhM4TR77r2ngVexEvtZISxyAsyWdqTcjhm4CNILTcRuL3T7f2wVAvIDWe2V5jxi7fzi8-JBXn5x8S_6FYBV1dQPGwd0WN8Bag4542VC468bKf8kcBnVdIGVWpE9ZcyxZzl/s1600-h/AVANA2.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 268px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEJwAj1srpG_VhM4TR77r2ngVexEvtZISxyAsyWdqTcjhm4CNILTcRuL3T7f2wVAvIDWe2V5jxi7fzi8-JBXn5x8S_6FYBV1dQPGwd0WN8Bag4542VC468bKf8kcBnVdIGVWpE9ZcyxZzl/s400/AVANA2.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345266418227285282" /></a><br /><br />3) Go to Alignment\Create Subset<br /><br />4) In the window, Source Alignment: Master Alignment, choose DENV1 as serotype and C as protein, and give a name to the subset (e.g. DENV1_C)<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgv5Pr6YqGdIcv4lae7Hn4jb2KPW0dftcjpnmwzbFYz-5fVCGZ429IwPlu3XCSpj_mXcqQG6CgC8_Ids3TzcwPNiERks-07PpoCRmhO2qwIVvGshDdIXbmRSVGbXyK5sjx9htllL0vJGitf/s1600-h/AVANA3.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 268px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgv5Pr6YqGdIcv4lae7Hn4jb2KPW0dftcjpnmwzbFYz-5fVCGZ429IwPlu3XCSpj_mXcqQG6CgC8_Ids3TzcwPNiERks-07PpoCRmhO2qwIVvGshDdIXbmRSVGbXyK5sjx9htllL0vJGitf/s400/AVANA3.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345267886456443938" /></a><br /><br />5) Create the next subset by repeating step 4, but this time highlight the rest (DENV2,DENV3 and DENV4) as serotype, and give another name to the subset (e.g.DENV234_C)<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWpasDfku32BL44hgLD2cj9CJKA3hUy6VvRg6Ab0Lre7clapdXyy4JonVP685S8s_e5qqDIM_RZQTTI6l2PiY_rcYtKpGsMPrkE4F97Gp3mJbzBf5cLGeBJOQTRWJlmw9Y3U3SLt7KSELa/s1600-h/AVANA4.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 268px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWpasDfku32BL44hgLD2cj9CJKA3hUy6VvRg6Ab0Lre7clapdXyy4JonVP685S8s_e5qqDIM_RZQTTI6l2PiY_rcYtKpGsMPrkE4F97Gp3mJbzBf5cLGeBJOQTRWJlmw9Y3U3SLt7KSELa/s400/AVANA4.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345268000818968834" /></a><br /><br /><br />6) Check that the sample size is 9 by going to Tools\Preferences. It will scan for peptides of length 9 which is the typical length of t-cell epitopes.<br /><br />7) In the same window, under the "Comparisons" tab, tick "Estimate average mutual information" and set the MI threshold to 1.000 (ideally we want value of 1, if get nothing then we consider other thresholds).<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUZ936bJXqO1rML-T0EBBsQM0pK1TjlBFx0s4Omi1BW1UTJLfQhjT-uJkqfNL9ZL3O1SpigMfnZuJxyzOw_RJilskd3UcUH_sgGf-Zc-oChOQ9lplAWgX0sB9LlLycLcuTZk1ssHAW92KA/s1600-h/AVANA5.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 267px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUZ936bJXqO1rML-T0EBBsQM0pK1TjlBFx0s4Omi1BW1UTJLfQhjT-uJkqfNL9ZL3O1SpigMfnZuJxyzOw_RJilskd3UcUH_sgGf-Zc-oChOQ9lplAWgX0sB9LlLycLcuTZk1ssHAW92KA/s400/AVANA5.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345268152508114018" /></a><br /><br />8) Next, go to View\Compare two alignments.<br /><br />9) Click DENV1_C as top alignment and DENV234_C as bottom alignment<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEis_N4Qk8761X0LOgsif38AXqJ4w3Z5Pb-6Wg9DUwlV4OCBV2nKKtniGbgxaDGKymhMtZQkaRUC33JiAysoOwajZDbyyL8peNGTVcNrab2qJi89XDuPXZs8yJn3jWUeYcQTC9eWoZNoS4zm/s1600-h/AVANA6.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 268px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEis_N4Qk8761X0LOgsif38AXqJ4w3Z5Pb-6Wg9DUwlV4OCBV2nKKtniGbgxaDGKymhMtZQkaRUC33JiAysoOwajZDbyyL8peNGTVcNrab2qJi89XDuPXZs8yJn3jWUeYcQTC9eWoZNoS4zm/s400/AVANA6.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345268266499537106" /></a><br /><br />10) You will see two graphs. Go to View\Show Mutual Information and View\Show sequence logo.<br /><br />11) The green line in the graph shows the mutual information. MI value tells u what is characteristic in one alignment when compared to the other alignment. MI value of 1 means, it is seen in this alignment, but was not seen in the other alignment.<br /><br />12) Click on the position numbers to your left to see the sequence logo, which shows conservation and all the peptides at that position.<br /><br />13) Export your results by going to View\Statistics\Diversity and save as .txt. Create an excel sheet for better viewing. Sort them according to descending MI, then increasing entropy.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYjjSy9X77P481NREbetmCd7SL4uTi8QX_idF03GsVoZJg3EJcN2_Te6KknoI50dyoU-khI8wRmSkKCZxZTZjdT9sVtWoiZ-BIiLaDXGTEMe_NSztcPbkXZyM8eq2rXR9A8olE_qfMrfRr/s1600-h/AVANA7.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 267px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYjjSy9X77P481NREbetmCd7SL4uTi8QX_idF03GsVoZJg3EJcN2_Te6KknoI50dyoU-khI8wRmSkKCZxZTZjdT9sVtWoiZ-BIiLaDXGTEMe_NSztcPbkXZyM8eq2rXR9A8olE_qfMrfRr/s400/AVANA7.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5345268439726655346" /></a>^BeNBeN^http://www.blogger.com/profile/11629878814774576609noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-3244568326159718192009-06-02T12:03:00.004+08:002009-06-02T12:11:58.084+08:0024) Summary steps in activating LAN connection in VMWare if problems still occur after post 22Comment by Jean:<br /><br />Summary steps in activating LAN connection in VMWare if there are still problems in connecting online (after post 22):<br /><br />a) lspci -vvv and ifconfig -a (display output below, checking what hardware the VMplayer is running from)<br /><br /><code><br /> 02:01.0 Multimedia audio controller: Ensoniq ES1371 [AudioPCI-97] (rev 02)<br /> Subsystem: Ensoniq Creative Sound Blaster AudioPCI64V, AudioPCI128<br /> Control: I/O+ Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-<br /> Status: Cap- 66MHz- UDF- FastB2B+ ParErr- DEVSEL=medium >TAbort- TAbort- <MAbort- >SERR- <PERR- INTx-<br /> Latency: 64 (1500ns min, 63750ns max)<br /> Interrupt: pin A routed to IRQ 19<br /> Region 0: I/O ports at 2080 [size=64]<br /> Kernel driver in use: ENS1371<br /> Kernel modules: snd-ens1371<br /><br /> 02:02.0 USB Controller: VMware Inc Abstract USB2 EHCI Controller (prog-if 20 [EHCI])<br /> Subsystem: VMware Inc Abstract USB2 EHCI Controller<br /> Control: I/O- Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-<br /> Status: Cap- 66MHz- UDF- FastB2B- ParErr- DEVSEL=fast >TAbort- TAbort- <MAbort- >SERR- PERR- INTx-<br /> Latency: 64 (1500ns min, 63750ns max)<br /> Interrupt: pin A routed to IRQ 16<br /> Region 0: Memory at e8900000 (32-bit, non-prefetchable) [size=4K]<br /> Kernel driver in use: ehci_hcd<br /><br /> eth1 Link encap:Ethernet HWaddr 00:0c:29:bf:37:04<br /> BROADCAST MULTICAST MTU:1500 Metric:1<br /> RX packets:0 errors:0 dropped:0 overruns:0 frame:0<br /> TX packets:0 errors:0 dropped:0 overruns:0 carrier:0<br /> collisions:0 txqueuelen:1000<br /> RX bytes:0 (0.0 B) TX bytes:0 (0.0 B)<br /> Interrupt:18 Base address:0x2024<br /><br /> lo Link encap:Local Loopback<br /> inet addr:127.0.0.1 Mask:255.0.0.0<br /> UP LOOPBACK RUNNING MTU:16436 Metric:1<br /> RX packets:210 errors:0 dropped:0 overruns:0 frame:0<br /> TX packets:210 errors:0 dropped:0 overruns:0 carrier:0<br /> collisions:0 txqueuelen:0<br /> RX bytes:424561 (414.6 KiB) TX bytes:424561 (414.6 KiB)<br /><br /></code><br /><br />b) dhcpcd -k eth1 (kill eth1)<br /><br />c) ifconfig eth1 up (restart eth1)<br /><br />d) dhcpcd -nd eth1 (do dhcp call and look for packet advertising the network server from the host, and if found, it will assign an IP address to eth1.)<br /><br />e) ifconfig eth1 (check that eth1 has an ip now)^BeNBeN^http://www.blogger.com/profile/11629878814774576609noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-9171032614275947382009-06-02T11:09:00.012+08:002009-06-02T11:49:03.883+08:0023) How to use MySQL in Proline???This is a simple tutorial on how to use mySQL commands in Proline. <br /><br />a) Firstly, log in to the server using putty.exe in Windows or SSH in BioSLAX using your username and password. (See post 2 if you have forgotten how to login through BioSLAX)<br /><br /><br />b) Next, log in to mysql (it may be a different username and password). See the screenshot below. You will directly enter the database denvdb.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiwJn5ygDL6-R5zeo-A4gwre4AouGrxhLYl49dgS-SCFlEn84K-Sat8SJIlCIe6BPkMBsf-432BbZTNAJc8vtocRij-qkRwXsZBwVPfPmdLlAg_JRMSV4fcdwymFUOsLERn9MNnrkE0s7OO/s1600-h/mysql.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 248px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiwJn5ygDL6-R5zeo-A4gwre4AouGrxhLYl49dgS-SCFlEn84K-Sat8SJIlCIe6BPkMBsf-432BbZTNAJc8vtocRij-qkRwXsZBwVPfPmdLlAg_JRMSV4fcdwymFUOsLERn9MNnrkE0s7OO/s400/mysql.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5342564871877612194" /></a><br /><br />c) Before proceeding, type "\h"(help) to take note of important commands required for navigation through mySQL. See the screenshot below:<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5Pytnu64LCPQFAX5x3vi5miBGorPpDkBCTIyA1X1PYkdZRrDGdnhg70OeRMBaTOB7OOmpUoCbtS8tirf9EOVuOzAT1jQ1b6NlS0O46I3uT5aNP2zmBfPk6vdWwkUdfwjPFi0PbxJ2qNp-/s1600-h/mysql2.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 349px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5Pytnu64LCPQFAX5x3vi5miBGorPpDkBCTIyA1X1PYkdZRrDGdnhg70OeRMBaTOB7OOmpUoCbtS8tirf9EOVuOzAT1jQ1b6NlS0O46I3uT5aNP2zmBfPk6vdWwkUdfwjPFi0PbxJ2qNp-/s400/mysql2.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5342566989215645762" /></a><br /><br />Some important commands are:<br /><br />1) \g, \G : type either of these commands to send an SQL query to the server. \G displays results vertically.<br /><br />Example: \g SELECT * FROM DENV (display all data in the table DENV). Note that you need to enter the same command twice. See the screenshot below:<br /><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0_6nR83VwNJTxCbSce0NhnW18SgtQWCjYQ3wTWgqNfOVQmownMizE2-g6dzX__f7bTMvcEBbx8RQZxB8R-ccBQH4IYelR1v0nZZtJP1wmidcDx04ehgngxWSC_jWWsPLQ2pzn4erju81c/s1600-h/mysql3.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 247px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0_6nR83VwNJTxCbSce0NhnW18SgtQWCjYQ3wTWgqNfOVQmownMizE2-g6dzX__f7bTMvcEBbx8RQZxB8R-ccBQH4IYelR1v0nZZtJP1wmidcDx04ehgngxWSC_jWWsPLQ2pzn4erju81c/s400/mysql3.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5342569191303427826" /></a><br /><br /><br />2) \c : Clear cache. After an SQL query, use this command if you want to enter another query.<br /><br /><br />3) \q: Quit mySQL to log back to proline.<br /><br /><br /><br />Notes:<br /><br />For uploading a table with data to mySQL, you can use the method on post 4. Otherwise, you can create an empty table with just your fields in the columns using the CREATE keyword. Note that there are many keywords to use in mySQL. You can refer to <a href="http://www.tutorialsweb.com/sql/working-with-mysql.htm">here</a> for more tutorials on mySQL.<br /><br /><br /><br />Two keywords that may be important are:<br /><br />a) Syntax for changing the data types of a column:<br /><br />ALTER TABLE table_name MODIFY column_name type<br /><br />Example: \g ALTER TABLE Registration MODIFY contactno INT(10)<br /><br /><br />b) Syntax for showing column fields, data type, field attributes, primary key and other information in a table:<br /><br />SHOW columns from table_name<br /><br />Example: \g SHOW columns from DENV^BeNBeN^http://www.blogger.com/profile/11629878814774576609noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-50628000274468315652009-05-04T17:05:00.003+08:002009-06-01T17:02:57.824+08:004) Exporting SQL database from Bioslax and importing to another server's SQL databaseTo export SQL database from Bioslax and import to another server's SQL database (e.g. proline.bic.nus.edu.sg)<br /><br />a) Type the following command in Bioslax Konsole:<br />#mysqldump -u username -ppassword database_name > FILE.sql<br /><br />e.g #mysqldump -u root -phahahaha DENVDB > FILE.sql<br /><br />FILE.sql would be generated in /root. Copy the file to Windows Desktop just in case.<br /><br /><br />b) Type the following command in Putty Konsole or SSH in Bioslax Konsole (server side):<br />#mysql -u username -ppassword database_name < FILE.sql<br /><br />e.g #mysql -u benjamin -phahahahah denvdb < FILE.sql<br /><br />Justin has created the database as denvdb.<br /><br />Got an error message:<br />ERROR 1045 (28000): Access denied for user 'benjamin'@'localhost' (using password: YES)<br /><br />Justin has enabled CREATE and ALTER access for my account, so it works now.<br /><br /><br />Tips from Justin:<br /><br />1. don't type your password on to a command line ... people can just see what you are typing by using commands such as finger or who <br />e.g. instead of typing ...<br />#mysqldump -u username -ppassword DENVDB > FILE.sql<br /><br />type<br />#mysqldump -u username -p DENVDB > FILE.sql<br /><br /><br />then the system will prompt you for a password and then only you type in there (it won't be shown on the screen as you type, so no worry)<br />also, by typing your pass on the command line, others can easily just check your ~/.bash_history file to see what you have typed and hence get your pass<br /><br /><br />2. in Windows, it is not case sensitive since it doesn't have much concept of case sensitivity ... in Linux, UNIXes etc<br />yes it matters. So, preferably you just use small case for most things (if possible) ... and try not to use spaces in between names as well ...<br />it will make a lot of things easy .. besides, you need less effort following this simple convention.<br /><br />3. before you try to do loading and stuffs, you can always check with account login first.<br />just login to proline and type<br /><br />mysql -u benjamin -p<br /><br /><br />this way you can test to see if you can even login or not in the first place ... and if yes, then you can narrow down what went wrong. <br />Anyway, assuming that you managed to get in as what I've done using ur account, you will see there are two databases ...<br />one is denvdb the other is information_schema. The latter is a system default so ignore that.<br /><br /><br />with that, then next thing is ... in your FILE.sql ... do you have a statement like<br /><br /><br />use denvdb;<br /><br /><br />right at the top of the file ?<br />if you don't , then you have to do <br /><br /><br />mysql -u benjamin -p denvdb < file.sql^BeNBeN^http://www.blogger.com/profile/11629878814774576609noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-79336457956016452162009-05-19T21:29:00.006+08:002009-05-21T04:05:40.935+08:0022) How to fix your internet connection in BioSLAX VMWareThis tutorial is for those who when after booting up their BioSLAX VMWare find that the internet is not working. For example, you ran Firefox and could not access any website, or ping any site through the Konsole, or could not get the "Wireless Assistant client" to assist you (it returned "No usable wireless device found, wireless, Wireless Assistant will quit now"). You can try the steps listed below to solve this problem: <br /><br />1. Select the "Bridged" network adaptor (select from the Devices menu on top of the screen) if you are using wired internet. For wireless internet, use the "NAT" adaptor, which forces the virtual machine to talk to the network address card of the host machine, so that the host acts as a router.<br /><br />2. Type the following in the Konsole to check if your dhcp client is up and running<br /><code><br />ps -ef | grep dhcp<br /></code><br /><br /># This check the process (ps) number of the dhcp, and if it is running it will be shown as one of the processes. If you have two or more dhcp processes, choose the one corresponding to eth1 if wireless network is desired or eth2 for wired network.<br /><br />3. If the dhcp is running, kill it to reset things. For example,<br /><code><br />kill -9 4663<br /></code><br /><br /># Assuming 4663 is the process number of the eth1 dhcp that is to be terminated.<br /><br /><b>Note</b>: You can kill dhcp and bring down the interface for various interfaces using "dhcpcd -k <interface>", e.g. <br /><code><br />dhcpcd -k eth1 or dhcpcd -k wlan0<br /></code><br /><br />There is no need to do ps -ef and killing of the process.<br /><br />4. After killing the dhcp, you want to check whether the eth1 or 2 card is being recognized by BioSLAX. Type<br /><code><br />ifconfig -a <br /></code><br /><br /># If the interface card (eth1 or 2) is listed, along with the loop back, this means that the eth1 (or 2) card is recognized by Bioslax. Now, to check whether the eth1 (or 2) card is up and running, type<br /><code><br />ifconfig<br /></code><br /><br /># If you only see loop back, then it means that your eth1 (or 2) card is not running. You need to start the eth1 (or 2) by typing<br /><code><br />ifconfig eth1 up<br /></code><br /><br /># Change eth1 to 2 if you want to up eth2<br /># If desired, you can bring eth down in the same manner<br /><br />5. Once the eth1 (or 2) is up and running. You need to start the dhcp. Type<br /><code><br />dhcpcd -nd eth1 <br /></code><br /><br /># This will do dhcp call and look for packet advertising the network server from the host, and if found, it will assign an IP address to eth1. When successful, the connection established will pop up, courtesy of the BioSLAX GUI.<br /># For eth2, change eth1 to 2<br /><br />You are done!<br /><br /><i>Summary code</i><br /><code><br />1. dhcpcd -k eth1<br />2. ifconfig eth1 up; dhcpcd -nd eth1<br /></code><br /><br /><b>Note</b><br />If you are not running bioslax with persistence change saving mode, you will need to redo this step every time you reboot BioSLAX.Asif M. Khanhttp://www.blogger.com/profile/08184259065143974222noreply@blogger.com0tag:blogger.com,1999:blog-1737804828852994104.post-53567574757457597652009-05-08T03:55:00.001+08:002009-05-17T18:53:58.783+08:0011) How to burn an ISO file (e.g. BioSlax.iso) into a bootable Live CD/DVD<div>To burn an ISO file (such as BioSlax.iso) into a bootable Live CD/DVD , you should use a CD/DVD burning program with an image file creating/editing/extracting capability, such as CDBurnerXP, which is available for free at http://cdburnerxp.se/ and works on Windows 2000/XP/2003/Vista.<br /><br />Follow these step by step instructions to burn an iso file:<br /><br />1 Download and install the CDBurnerXP program from http://cdburnerxp.se/.<br /><br />2 Run CDBurnerXP Program, change to “Burn ISO image” option, click “OK”.<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtBpo7AvP11C_GJtVUY-tAnB5muCFu0fbUmy9CIbrBGyUJbqZLpAcCVmJiS8AAsFAw5drSfzHegXlBX8C3Wu4fH8B7XMxGWiqnPdlV5GMl-WEhnz8LdDGYoEL0xKd10eNgxcesKsb1-sxn/s1600-h/image003.jpg"><img id="BLOGGER_PHOTO_ID_5333090785523747634" style="WIDTH: 363px; CURSOR: hand; HEIGHT: 272px" alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtBpo7AvP11C_GJtVUY-tAnB5muCFu0fbUmy9CIbrBGyUJbqZLpAcCVmJiS8AAsFAw5drSfzHegXlBX8C3Wu4fH8B7XMxGWiqnPdlV5GMl-WEhnz8LdDGYoEL0xKd10eNgxcesKsb1-sxn/s400/image003.jpg" border="0" /></a><br /><br />3 Insert a blank CD-R/DVD-R to your CD/DVD R/W drive, load the ISO image file. Select the options as shown below then click on the “Burn disc” button.<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKSoo6P7NnRPCl2MWFnZNTPxidDcO_zpFjPGMNwr75ouz-z7bIvyrJU3hcmgxV7_gxyKVdD1LGloS7Y8-Y5VuaInz2Tjcm7kIyZ0tfA-cmHbAqAgqjUkELLMQBXvgjDt30yCUJ4jS96ozX/s1600-h/image006.jpg"><img id="BLOGGER_PHOTO_ID_5333091143184682738" style="WIDTH: 400px; CURSOR: hand; HEIGHT: 273px" alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKSoo6P7NnRPCl2MWFnZNTPxidDcO_zpFjPGMNwr75ouz-z7bIvyrJU3hcmgxV7_gxyKVdD1LGloS7Y8-Y5VuaInz2Tjcm7kIyZ0tfA-cmHbAqAgqjUkELLMQBXvgjDt30yCUJ4jS96ozX/s400/image006.jpg" border="0" /></a><br /><br />4 You should see this once if the writing process get started.<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxyuJbBM9XkZFAClgk3DdBpYj3bcVk_uDFgSiLpW5kMWCAIjcpdp-jVNX3z4gdgcuKzBWiSPL-77Mov2VROls4InCz_vxSoQ6jqhBPATGJZToELgB00SIJLBD0kTXqC_HhMhC7d0qCOXGS/s1600-h/image008.jpg"><img id="BLOGGER_PHOTO_ID_5333091405351090786" style="WIDTH: 400px; CURSOR: hand; HEIGHT: 280px" alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxyuJbBM9XkZFAClgk3DdBpYj3bcVk_uDFgSiLpW5kMWCAIjcpdp-jVNX3z4gdgcuKzBWiSPL-77Mov2VROls4InCz_vxSoQ6jqhBPATGJZToELgB00SIJLBD0kTXqC_HhMhC7d0qCOXGS/s400/image008.jpg" border="0" /></a><br /><br />5 if you see a message as below, you have successfully created a copy of the BioSLAX Live CD/DVD from the image that you downloaded!<br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimIsDWBIisZJxQppLROsK98R_7e4AA4COeZ4TArBaF28egv1LqMJhCvnICu15cSI6FvCYOiHP2JMHCbYshRI1Iqt38KQEm-MS7Rd96oBKhhwyoEKCDggiVb8WG8V_WCX4hepA7VK-m7pSr/s1600-h/image010.jpg"><img id="BLOGGER_PHOTO_ID_5333091663243221938" style="WIDTH: 400px; CURSOR: hand; HEIGHT: 139px" alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimIsDWBIisZJxQppLROsK98R_7e4AA4COeZ4TArBaF28egv1LqMJhCvnICu15cSI6FvCYOiHP2JMHCbYshRI1Iqt38KQEm-MS7Rd96oBKhhwyoEKCDggiVb8WG8V_WCX4hepA7VK-m7pSr/s400/image010.jpg" border="0" /></a> </div><br /><div> </div><br /><div> </div><br /><div> </div><br /><i><div>Content by: Asif M. Khan </div><br /><div>Posted by : Sye Bee & Asif M. Khan</div><br /><div>Edited by : Sye Bee & Asif M. Khan</div></i>cbeehttp://www.blogger.com/profile/13749285444941751919noreply@blogger.com0