[Bioperl-l] Perl script to extract from ncbi

Cui, Wenwu (NIH/NLM/NCBI) [C] cuiw at ncbi.nlm.nih.gov
Fri Feb 9 09:20:10 EST 2007

This is an example for fetching two GenBank records
(id=124504630,110665734) in XML format. Organism names like
'<GBSeq_organism>Rattus norvegicus</GBSeq_organism>' can be parsed from
the XML. 





Or you can get TaxIds and translate them into real names:



Wenwu Cui, PhD


-----Original Message-----
From: George Heller [mailto:george.heller at yahoo.com] 
Sent: Thursday, February 08, 2007 1:55 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Perl script to extract from ncbi


Hi all, 


  I have a question regarding extracting data from Ncbi. I have a
database to store the sequence data, but the files I have loaded into
it, dont have a proper description line specified. Based on the
accession number, I need to find out what is the genus and species name
() from ncbi. 


  I have about 1500 records for which I need to extract the names from


  Any ideas of how I can go about writing a perl script for extracting
this information from ncbi?







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