[Bioperl-l] NCBI Genbank ID to TaxonID via Bioperl?

Nathan Haigh n.haigh at sheffield.ac.uk
Wed Jun 22 03:51:30 EDT 2005

Atlas Web tools also provide a web based service that is capable of doing


They use the gi2taxonid file from ncbi as mentioned by Jason. I personally
create a DB_File of the gi2taxonid file - if your working with a species for
which sequences are being rapidly sequenced you'll have to download the file
on a regular basis to ensure the new GI numbners are mapped to a taxonid.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Michael Spitzer
Sent: 21 June 2005 14:28
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] NCBI Genbank ID to TaxonID via Bioperl?

Dear All,

For a list of approx. 20 GI numbers (NCBI GenBank IDs) I need the taxon 
ID as given in the corresponding full GenBank record. Which is the 
easiest way to accomplish this task automatically? Does Bioperl help? 
Can one access this function via the NCBI website (possibly, using 
Bioperl)? Or, does one have to download the whole GenBank database?

All I could find out is that there is a function 'gi2taxid' in the NCBI 
toolkit, but I have no experience with using the toolkit, and I hope 
that there is an easier 'Bioperl' way to solve the problem - could 
BIO::DB::NCBIHelper be the way to go? Any help or hints are greatly 

Kind regards,

Michael Spitzer
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Bioperl-l at portal.open-bio.org

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