[Bioperl-l] GFF3 - Bioperl - SO

Steffen Grossmann grossman at molgen.mpg.de
Mon Oct 11 09:20:47 EDT 2004

Dear all,

I fancy very much the approach taken by SO(FA) 
(http://song.sourceforge.net/) to standardize the vocabulary used for 
sequence annotation. Also, the GFF3 format is a nice way to represent 
SO-compatible annotations and it would be a great thing to have this all 
working seamlessly with bioperl.

A first step towards such a seamless integration into bioperl would be a 
parser which is able to read/write hierarchically nested feature 
collections from/to GFF3 files. Such a parser should make use of the 
GFF3 specific 'ID' and 'Parent' tags.

Of course, I know about the 'Bio::Tools::GFF' and 
'Bio::SeqFeature::Tools' modules, where some related stuff can be found. 
The problem is that the 'Bio::Tools::GFF' module doesn't respect the 
'Parent' and 'ID' tag structure and grouping in the 'Unflattener' 
approach is also done conceptually different.

Does anybody know about whether there is someone working on such a 
project? Or, if there is no such project, is someone interested in 
joining to start it?

Thanks in advance for any response!


%            Steffen Grossmann                %
%                                             %
% Max Planck Institute for Molecular Genetics %
%      Computational Molecular Biology        %
%              Ihnestrasse 73                 %
%               14195 Berlin                  %
%                 Germany                     %
%         Tel: (++49 +30) 8413-1167           %
%         Fax: (++49 +30) 8413-1152           %

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