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BioPerl Remote Blast with Gene ID only ?

I'm new to BioPerl. I've been reading the howtos and looked at sample scripts, but it doesn't seem that I can run a blast using gene Ids only? I've been looking and it doesn't really mention that. I just wanted to know if it can be done and a sample syntax?

bioperl blast
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updated by Ram Ram • written by ksi216 • ksi216

1 answer

BLAST is a sequence comparison tool, so no, you can't pass only an ID. You'll need to pull out the sequence first and then pass it to the RemoteBlast module. You can fetch a list of sequences from Genbank (check out the efetch HOWTOs) with bioperl and then run the BLAST search. That would be my suggestion based on what you have provided.

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written by SES SES

is there any website that I can input Gene Id's and it will give me Fasta sequences ?

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written by ksi216 • ksi216

Sorry, I missed your comment. Of course you can search by ID but the place you'll want to search depends on the ID source (e.g., Uniprot or Genbank). Once you get a list, you can do that with a BioPerl as I mentioned.

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written by SES SES

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