[Bioperl-l] SeqIO (stress) testing

Hilmar Lapp hlapp@gmx.net
Wed, 20 Dec 2000 10:51:41 -0800

Kris Boulez wrote:
> Quoting Hilmar Lapp (hlapp@gmx.net):
> > Kris Boulez wrote:
> > >
> > > - starting from t/test.genbank, writing a swiss-prot file gives (we die,
> > >   no error thrown)
> >
> > test.genbank is DNA. Do you translate it?
> >
> Nope, checked test.fasta to be protein, forgot this one.
> Should this matter (i.e. does Swissprot checks it is writing a protein
> sequence) ?

Probably it shouldn't matter. But I can imagine that you run into
trouble if you try to write a Genbank feature table in Swissprot format.
One should check what the problem is though. Significant information
loss is, however, almost unavoidable. E.g. in Genpept you have active
site and a binding site both annotated as site, and a tag site_type
tells you what sort of site it is. In Swissprot both sites would have
different keys, and there are no tags apart from 1 note-like comment.


Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757