Retrieve batch subject span FASTA

Question

[kgousset]

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?

Answer 1

[Siva]

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

Have a look at my previous post.