[Bioperl-l] retrieving by acc from a local multifasta file

[Remo Sanges]

On Aug 6, 2004, at 12:50 PM, Maria Persico wrote:

> Hi All,
>
> This may be a stupid problem but for me it's something difficult:
> I have a list of swissprot accessions(my_acc) and I want to extract 
> from
> uniprot_sprot.fasta only sequences of my list.
> How can do this with bioperl?

Hi Maria,

you could create an index of your fasta file
and then retrieve sequences from it.

Read the tutorial section 'III.1.2 Indexing and accessing local 
databases'
http://bioperl.org/Core/Latest/bptutorial.html

and the documentation of Bio::Index::Fasta module
http://doc.bioperl.org/releases/bioperl-1.4/Bio/Index/Fasta.html

HTH

Remo