[Bioperl-l] pfam query

[Juan Carlos Sanchez Ferrero]

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);

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



print  STDERR "$pfam\n";




$query= $pfam.'Q9P902'

system "wget -p $query";

exit;

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

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

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


jc




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
>