[Bioperl-l] NCBI Genbank ID to TaxonID via Bioperl?
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.
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?
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
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
More information about the Bioperl-l