Bioperl: Bio* integration with AceDB

[Matthew Pocock]

Hi

> > We then need a sequence transducer class (subclassed from Bio::SeqIO) that
> > reads/writes Bio::Perl objects and .ace files and translates between them.
> >
>
> The Bio::SeqIO::ace would be great. Also viewing an AceDB as a
> Bio::DB::SeqI (a sequence database) would also be great. If that was done
> the "for free" you would get a biocorba server implemented in Perl , as
> the bioperl corba server is written to work on top of the Bio::DB::SeqI
> interface (jason - feel free to correct me!)
>

There is an example program in BioJava under demos/acedb called ServeAceAsCorba
that serves the sequences (or some sub-set) from an AceDB database as a BioCorba
seqDB object, which you can interact with from Perl. It uses the acedb socket
client with connection-pooling & full support for multi-threaded server-client
interactions (even handles the case where an ace socket times out for you!).
Does this sound like a starting point?

>> Anyone interested, reply to me, or post to BioPerl.

> >
> > Dave Block
> > NRC PBI Saskatoon
> >
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