[Bioperl-l] Retrieving sequence from local blast database

[Brian Osborne]

Anthony,

You probably want to use Bio::DB::Fasta, it offers methods like
get_Seq_by_id() to get sequences out of multiple fasta files. This module is
described in bptutorial.pl as well as its cousin, Bio::Index::Fasta. Hint:
"use strict". We ran into some trouble recently using these when we didn't.

Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of AUnderwood@PHLS.org.uk
Sent: Tuesday, July 30, 2002 4:26 AM
To: Bioperl-l@bioperl.org
Subject: [Bioperl-l] Retrieving sequence from local blast database

HI all,

Does anyone know if there is a method within bioperl to retieve the sequence
of an entry from a local blast database formatted with the formatdb command.
I have retrieved a hit with the standalone blast method and want to retrieve
all the sequence of the hit. If I use $hit->next_hsp->hit_string then then
sequence retrieved is often not the entire sequence of the hit. Is it
possible to use the accession number retrieved from the hit to retrieve the
sequence from the local databse or just retrieve the entire hit sequence.

Many thanks

Dr Anthony Underwood
Bioinformatics Unit
Central Public Health Laboratory
61 Colindale Avenue
London
NW9 5HT
t:    0208 2004400 ext. 3618
f:    0208 3583138
e: aunderwood@phls.org.uk



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