Wednesday, May 13, 2009

19) How to remove duplicate sequences from a fasta formatted input file

===Update: 21 March 2011===

For a more comprehensive and updated information on this, please see Post 32.
Read all the way to the end of that post.

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You can use Jalview to easily check for duplicates and remove them if any.

1. Download and install Jalview on your home system from

http://www.jalview.org/download.html



2. Run Jalview and close all example windows



3. Load your fasta file to Jalview



4. Remove duplicates:

- Select all sequence

- Go ‘Edit’ to uncheck the pad gaps function.

- In ‘Edit’, select ‘Remove all gaps’

- After that select ‘Remove redundancy’

- At the “redundancy threshold selection” dialog box, set the threshold value to 100, click ‘Remove’.



5. Saving the unique fasta file and you are done!




Content by: Asif M. Khan & Sye Bee
Posted by: Sye Bee
Edited by: Asif M. Khan
Posted by at

3 comments:

  1. UnknownMay 8, 2010 at 5:03 AM

    great, I like it!

    ReplyDelete
  2. AnonymousOctober 8, 2011 at 12:47 AM

    Thank ya for the help

    ReplyDelete
  3. Eslam SamirFebruary 18, 2017 at 4:01 PM

    Here is my free program on Github **Sequence database curator**
    (https://github.com/Eslam-Samir-Ragab/Sequence-database-curator)

    It is a very fast program and it can deal with:

    1. Nucleotide sequences
    2. Protein sequences

    It can work under Operating systems:

    1. Windows
    2. Mac
    3. Linux

    It also works for:

    1. Fasta format
    2. Fastq format

    Best Regards

    ReplyDelete

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