[Bioperl-l] BLAST AND SEQUENCE RETRIEVAL

[Heikki Lehvaslaiho]

Pedro,

Have a look at bioperl modules at Bio::DB. The one your need for most blasts
outputs is Bio::DB::GenBank.

>From the synopsis:

   use Bio::DB::GenBank;
   $gb = new Bio::DB::GenBank;

   $seq = $gb->get_Seq_by_id('MUSIGHBA1'); # Unique ID
   $seq = $gb->get_Seq_by_acc('J00522'); # Accession Number
   $seq = $gb->get_Seq_by_gi('405830'); # GI Number

Bio::DB::GenPept works exactly the same way.

	-Heikki

Pedro A Reche Gallardo wrote:
> 
> Hi all, I know that is possible to use the bioperl modules to parse a
> blast output result taking the GI of the sequences, but  I wonder if there
> is a procedure for retrieving the corresponding sequences from a local or
> remote database. It will be great if I someone could show me how to do
> this.
> Best regards,
> 
> Pedro Reche
>  ***************************************************************************
> PEDRO a. RECHE gallardo, pHD            TL: 617 632
> 3824
> Scientist, Mol.Immnunol.Foundation,     FX: 617 632 3351
> Dana-Farber Cancer Institute,           EM:
> reche@research.dfci.harvard.edu
> Harvard Medical School,                 EM:
> reche@mifoundation.org
> 44 Binney Street, D610C,                URL:
> http://www.reche.org
> Boston, MA 02115
> ***************************************************************************
> 
> 

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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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