[Bioperl-l] NCBI Genbank ID to TaxonID via Bioperl?
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Tue Jun 21 10:27:36 EDT 2005
Bio::DB::Query::GenBank can be used to query GenBank, and Bio::DB::GenBank can be used to retrieve records.
After that it depends where the taxon id is stored - if it is stored in the feature table, as in:
Then once you have the Bio::Seq object from Bio::DB::GenBank you can iterate through the feature table and look at each tag-value pair (using the "has_tag" and "each_tag_value" methods) to look for something like db_xref="taxon:39947"
From: bioperl-l-bounces at portal.open-bio.org on behalf of Michael Spitzer
Sent: Tue 21/06/2005 2:27 PM
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