[Bioperl-l] Reading all sequences using Bio::DB::Flat in SwissProtfile

[Brian Osborne]

Kenny,

Did you take a look at Bio/Index/Swissprot.pm? What's important for you will
be building the index using the keys you're interested in as opposed to the
default key, using the id_parser method. See the Bio::Index section in the
bptutorial for an example.

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 Daily,
Kenneth Michael
Sent: Wednesday, January 19, 2005 11:49 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Reading all sequences using Bio::DB::Flat in
SwissProtfile


I want to work with a local copy of the SwissProt database, and need to
search through all of the entries. I only see methods to return sequences by
accession. However, I cannot use just FASTA format of the SwissProt records,
as I need to use the feature fields. What I need to learn is how to do a DB
search on the features field of the SwissProt records, if its possible.
Would there be any advantage do doing it with the DB instead of just using
SeqIO as an input stream? I think it might, since every time I want to do a
search I must read in the entire file again, which is very costly. Thank
you.

Kenny Daily
Indiana University
School of Informatics
kmdaily [at] indiana [dot] edu

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