[Bioperl-l] Get GIs from Taxonomy ID

armendarez77 at hotmail.com armendarez77 at hotmail.com
Thu Jun 10 10:54:18 EDT 2010


Is there a BioPerl method that will give a list of GIs for a specified NCBI taxonomy Id?

I've previously tried using Urlapi to BLAST primers against the nr database on the NCBI server, but recently I keep getting a
'Bad Gateway' error.  While my system admin is looking into this, I've
decided to go another route.  Therefore, I've downloaded the NCBI nr database.

The problem I've run into is restricting the BLAST against the nr database to a subset of sequences.  The NCBI Blast tools have an option (-l) that does this, but it requires a list of GI's.  

When I was using Urlapi, I restricted sequences using Taxonomy Ids (Entrez Query).  Therefore, is there a way to get all GIs within a Taxonomy Id?  I've seen that woth Bio::Taxonomy I can give a GI and get a Tax Id, but not the reverse.

Thank you,


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