[Bioperl-l] pfam query

Juan Carlos Sanchez Ferrero jcsanchez at cib.csic.es
Thu Jun 16 11:33:54 EDT 2005

No is not that,
what i am more interested is in get the graphical representation of the 
domains of each of my prots
here is an example, i can do this:

#! /usr/bin/perl -w

use Bio::Tools::WWW qw(:obj);


print  STDERR "$pfam\n";

$query= $pfam.'Q9P902'

system "wget -p $query";


and it works fine,
but in contrast if i modify it in order to search for a seq

$pfam=$BioWWW->search_url('pfam_sp_uk');   to      

and the $query to something like $query=$pfam.'MTASDFPFCVLLIDFNPD..........'

i got an error saying that i haven't given a query sequence.....

maybe i am doing something wrong or maybe it is not possible do it this 
way, i don't know


Sean Davis wrote:

> On Jun 16, 2005, at 5:11 AM, Juan Carlos Sanchez Ferrero wrote:
>> hello,
>> Does anyone know if it is possible to make a batch query using 
>> bioperl to the pfam database ?
>> i tried using Bio::Tools::WWW,
>> but i am only able to get by the swisspfam accession number,
>> and what i am interested is in making new queries....
> I'm not sure what you are trying to do, but have you looked at ensembl 
> mart?  You can access the MySQL database running the ensembl mart 
> directly to query for genes with certain pfam domains or all pfam 
> domains for given (or all genes).
> Sean

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