[Biojava-l] Antw: Re: Exception thrown when parsing GenBank file

[Peter Cock]

On Wed, Nov 23, 2011 at 4:06 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
> Hi Dietmar,
>
> The GenbankLocationParser from biojava-1.8.1 is working perfectly as long as
> you feed him with DNA locations that use the syntax described in the
> DDBJ/EMBL/GenBank feature table definition.

As mentioned earlier, that document only covers nucleotide sequences,
not proteins as used in GenPept and the EMBL patents database:
http://lists.open-bio.org/pipermail/biojava-l/2011-November/007889.html

> What you've got (join(bond(9),bond(125))...) is a pseudo GenBank format
> that apparently describes protein structure and uses a slightly different
> syntax to indicate heteroatom locations. That is why you get all these
> exceptions thrown.
>
> George

It would be interesting to see if the EBI offer the same record(s) in
EMBL format, and if that too uses the (undocumented?) bond locations.

Peter