showfeat overlaping CDS

[David Bauer]

Peter Rice wrote:
> Internally the tags are stored with the first exon. They include an
> implicit group tag that can be displayed with the other exons. Is that what
> you need?

Yes, this would be nice. It would be clear which exon belongs to which
splice variant.
The feature display in showseq is similar.

> If you print out a feature table in GFF format (with seqretallfeat) what
> you see is pretty much what is stored internally. The Sequence and
> FeatFlags information is part of the feature data, rather than part of the
> tag-value list, and is used for keeping multiple exons together. For

What I get is a FeatFlags "0x100" for the first exon and a FeatFlags
"0x104" for the consecutive exons. The flags are the same for both CDS.
But the Sequence has a .## which differs between the two CDS. I think if
showfeat (and showseq) could show the complete tags with the first exon
and just the Sequence tag with the remaining exons with the -tags
option.

> We could probably add the Sequence tag to the showfeat output (although it
> is not part of the EMBL feature table) or we could duplicate all the tags
> if that's what users would prefer.

I think duplication of all tags is not necessary, the Sequence tag is
sufficient.

David.
-- 
Dr. David Bauer
GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus 
Robert-Roessle-Str. 10, D-13125 Berlin, Germany
bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151