[Bioperl-l] ProServer, a pluggable DAS server, Bio::SeqIO support added

[Andreas Kahari]

Hi lists (sorry for the cross-posting),

This for those of you who are interested in DAS but not aware of
ProServer:

ProServer is a DAS server implementation written in Perl by
Roger Pettett at the Sanger Institute, here outside Cambridge in
the UK.  It builds on top of ideas from Tony Cox, also at the
Sanger Institute.

The point with ProServer is that it is pluggable, so that any
data source may be used as a source to serve DAS features from,
as long as there is source adaptor and a transport module for
it.  There are source adaptors already written for a number of
types of sources, and they are fairly easy to extend to other
types of sources or transports (I recently wrote a toy "wgetz"
transport module from the already existing "getz" module which
is used by the Swissprot source adaptor).  Other DAS servers
often requires you to create a dedicated database of DAS data.

I thought it might be of interest to a couple of you to note
that you now also can serve features or sequence data from any
type of file that Bio::SeqIO can read.  This, of course, is
only of interest to people with smallish amount of data since
queries are looked up sequentially in the files (unless the
Bio::DB::Flat support in the code is used, which reduces the
lookup time but which doesn't support all formats).

ProServer is part of the Bio-Das2 module in the biodas CVS
repository:

    http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/Bio-Das2/?cvsroot=biodas



Cheers,
Andreas


-- 
|(--)|      Andreas Kähäri                                |<><>|
|-)(-|      EMBL, European Bioinformatics Institute       |><><|
|(--)|      Wellcome Trust Genome Campus, Hinxton         |<><>|
|-)(-|      Cambridge, CB10 1SD                           |><><|
|(--)|      United Kingdom                                |<><>|