[Bioperl-l] Bio::SeqIO::kegg

[Ewan Birney]

On Tuesday, October 21, 2003, at 02:46  am, Allen Day wrote:

> Hi all,
>
> I just added a parser for KEGG sequence records, available from:
>
> ftp://ftp.genome.ad.jp/pub/kegg/genomes/genes/
>
> I've parsed all tags except CODON_USAGE and POSITION into a
> Bio::Seq::RichSeq.  I didn't implement CODON_USAGE because I wasn't 
> sure
> what class would hold it, and also because the codon frequencies can be
> recalculated from the primary sequence.
>
> For the POSITION tag, I didn't implement it because I wasn't sure how 
> to
> deal with the reference sequence and exon positions for a spliced mRNA.
> If someone wants to explain to me how to do this, I'd be happy to
> implement it.  Or if someone wants to DIY, please feel free.
>
> I'm in the process of writing a parser for KGML:
>
> ftp://ftp.genome.ad.jp/pub/kegg/pathways/KGML_v0.3/
>
> to read in KEGG's pathway data, are people interested in representing
> metabolic networks in bioperl, or am I better off doing this as a 
> separate
> project?  Or better yet, has someone already done this?
>

Allen - whatever happens in Kegg parsing in bioperl, over at GK we'd 
like to
make sure that we can provide similar information and try to round trip
information. Imre Vastrik is the technical lead on GK and possibly
has some ideas about a generic "pathway" object model (GK has a rich
pathway object model which is defined in Protege and then Perl and
Java code run-time bind to the protege-generated and manipulated
datastructures).



> -Allen
>
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