Question: Retrieve batch subject span FASTA
0
gravatar for kgousset
5.2 years ago by
kgousset0
United States
kgousset0 wrote:

I just wanted to see if anyone might have a solution to a problem I am having with retrieving a batch of over 300 FASTA protein sequences.  I ran a BLAST search for a fragment of my protein of interest and now have a list of accession numbers with the subject spans of interest.  I know that I can retrieve batch sequences with "Batch Entrez," but it will return the entire sequence and I am only interested in the subject spans. It took me about an hour to retrieve 30 manually and I don't want to have to spend another 10 hours on this.  Might anyone know how to do this?

sequence • 1.5k views
ADD COMMENTlink modified 5.2 years ago by Siva1.7k • written 5.2 years ago by kgousset0
0
gravatar for Siva
5.2 years ago by
Siva1.7k
United States
Siva1.7k wrote:

You can get the subject sequence directly from BLAST with the option 'sseq'

Have a look at my previous post A: Blast+ results file parsing to fasta file .

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Siva1.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 984 users visited in the last hour