On Wed, Nov 23, 2011 at 4:06 PM, George Waldon <[email protected]> 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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
