[Bioperl-l] producing an organism report from BLAST results?

Jason Stajich jason.stajich at duke.edu
Mon Nov 21 16:26:23 EST 2005

Well isn't encoded in the hit name?
my ($gi)  = ($hit->name =~ /gi\|(\d+)/ );

If you run WU-BLAST you need to provide the -gi option on the command  

If you run NCBI-BLAST you need to provide the -I option

 From the blastall help:
   -I  Show GI's in deflines [T/F]
     default = F

On Nov 21, 2005, at 4:22 PM, Tim Reid wrote:

> You need to look up the taxonomid ID from the gi number for a record.
> thanks for your reply, but i am unable to find the gi number of a  
> blast hit.
> i have looked at the each_accession_number method in  
> Bio::Search::HitI, but it does not appear to yield a gi number.
> your help is appreciated.

Jason Stajich
Duke University

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