[Bioperl-l] Bio::Biblio

[Brian Osborne]

Susan,

Bioperl 1.2 supports Bio::Biblio->find, yes. You should show us the code
that's giving you the error message. Or try some of the examples in
examples/biblio/biblio_examples.pl.

By Pubmed citations "related" to a Genbank accession do you mean the
references found in the Genbank entry? If so then this is easily done using
Bioperl. First retrieve the sequence object for that accession number (see
the section in the bptutorial that discusses Bio::DB::GenBank), then get the
references using the Annotation methods. Perhaps this is not what you
meant...

Brian O.



-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Susan J. Miller
Sent: Wednesday, December 10, 2003 8:30 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Bio::Biblio

We are running Perl 5.6, Bioperl 1.2 on a Solaris8 machine.
A couple of questions about Bio::Biblio:

1. When I try to use the Bio::Biblio->find method I get an error message
saying that it is not implemented, yet looking in the bioperl list
archive I see replies that mention this method.  Should I be able to use
it?  Do I need a more recent version of BioPerl?

2. I would like to be able to take a Genbank accession number and find
any Pubmed citations that are related to the accession number.  NCBI
Entrez search will turn up Pubmed hits given an Accession number - is
there a way to do this using BioPerl?


--
Thanks,
-susan

Susan J. Miller
Biotechnology Computing Facility
Arizona Research Laboratories
Bio West 228
University of Arizona
Tucson, AZ  85721
(520) 626-2597

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