[Bioperl-l] Retrieving sequence from local blast database

[Jason Stajich]

On Tue, 30 Jul 2002 AUnderwood@PHLS.org.uk wrote:

> 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.
>
We can't read NCBI formatted index files (yet) plus they have been known
to change that format with different versions of blast so we're probably
not going to support it directly.

You can do instead, if you have the ncbi provided util 'fastacmd'

open(FAS, "fastacmd -s 'accessionnumber1,acc2,acc3' -d /path/to/db");
my $seqio =new Bio::SeqIO(-format => 'fasta',
			  -fh => \$FAS);

(make sure you formatted your db with 'formatdb -o T -i db ...')

Or you can alternatively index the db yourself with
Bio::Index::Fasta or Bio::DB::Fasta (two different implementations which
basically do the same thing - DB::Fasta does a bit more stuff)

-jason
> 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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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu