[Bioperl-l] Bio::DB::SwissProt

[Jason Stajich]

It is just waiting for someone to code it up. It requires a different, simpler approach. 

I don't have any time to do this but we welcome volunteers.  

The simple approach is just to open a file handle and use GET cmd to open the URL with the accession number per the msg I sent before. That filehandle goes to SeqIO and you don't need the Bio::DB module. 

You can also get Swissprot data via genbank DB handle. 

Jason Stajich
 

On Jul 20, 2011, at 4:23 AM, Oliver Schilling <oliver.schilling at mol-med.uni-freiburg.de> wrote:

> Dear Jason,
> 
> as thankfully pointed out by you on http://old.nabble.com/Fwd%3A-URGENT%21-Update-of-Bio%3A%3ADB%3A%3ASwissProt-td32059436.html#a32059436,
> 
> it seems that Bio::DB::SwissProt  is not supported by expasy any more. In a perl script, I used to access Swissprot data and annotations by
> 
> $sp = Bio::DB::SwissProt->new('-servertype' => 'expasy',
>                    '-hostlocation' => 'switzerland');
>                    $seq = $sp->get_Seq_by_id($id_swiss);
> 
> This of course does not work any more. Will Bio::DB::SwissProt  be adapted to the new expasy site in the near future?
> 
> Thanks a lot!
> 
> Oliver
> 
> 
> Dr. Oliver Schilling
> Group Leader & Emmy-Noether Research Fellow
> Institute for Molecular Medicine and Cell Research
> University of Freiburg
> Stefan-Meier-Str. 17, Room 02 027
> D-79104 Freiburg, Germany
> Tel: +49 761 203 9615
> email: oliver.schilling at mol-med.uni-freiburg.de