[Bioperl-l] getting only the aminoacids for a domain

José Ramón Blas Pastor joseramonblas at gmail.com
Wed Jul 14 03:38:04 EDT 2010


with these lines I download protein sequences matching "jjjj" uniprot code.

use lib '/sw/share/bioperl-pm588';
use Bio::SeqIO;
use Bio::DB::SwissProt;
$db_obj = Bio::DB::SwissProt->new;
$seq_obj = $db_obj->get_Seq_by_id('jjjj');

...from here, I cut the sequences and get only a piece of each one (with
subseq, between j1 and j2 residues)

$shortened = $seq_obj->subseq(j1,j2);
$seqio_obj = Bio::SeqIO->new(-file => '>jjjj.jletra.j1_j2.fasta', -format =>
'fasta' );

How can I download the sequence of ONLY THOSE AMINOACIDS that match, in
uniprot, in the Sequence annotation section,

Feature key: Domain
Description: lectin, ANK, Sushi,... the name of a given domain ?

Is there any way of downloading all the existing fasta sequences for a given

Thanks in advance,


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