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

Paulo Almeida paulo.david at netvisao.pt
Fri Aug 6 07:47:42 EDT 2004


If your fasta file is in a format that can be parsed by Bioperl, I think 
you just need to load the sequences into a Bio::Seq object, using 

( for details check 
http://search.cpan.org/~birney/bioperl-1.4/Bio/SeqIO.pm )

Then you can get the accesion number of each sequence with 
$seq->accesion_number and only retrieve those that match your list.

( for details check http://search.cpan.org/~birney/bioperl-1.4/Bio/Seq.pm )

Good luck,

Maria Persico wrote:

>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?

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