Friday, August 27, 2010

40) 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

>gi|34392270|emb|CAE46396.1| STAT_00044 Dd-STATb protein [Dictyostelium discoideum]

2. formatdb

formatdb -i input.fasta -p T -o T

3. In the /usr/local/wwwblast-2.2.17 folder of BioSLAX, backup blast.html and blast.cgi

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)

#!/bin/csh -f

#
# $Id: blast.cgi,v 1.1 2002/08/06 19:03:51 dondosha Exp $
#

echo "Content-type: text/html"
echo ""

#setenv DEBUG_COMMAND_LINE TRUE
setenv BLASTDB db





# I used my own database STATdb_Id as an example below.

5. Output example

2 comments:

  1. what do the parameter of blast.REAL mean?
    How could we fix for our own website?
    is it only for c shell?

    ReplyDelete
  2. It looks nice, but you did not precise what it the script for retrieve_record.php. Can you tell us?

    ReplyDelete