[Bioperl-l] Re: [SO-devel] Re: GFF3 preliminary

[Chris Mungall]

On Fri, 21 Feb 2003, Richard Durbin wrote:

> length
> just before the start of the ATG and after the stop codon.  There are SO
> terms for the start_codon and stop_codon but you really don't want to
> use them to define the start and end.  e.g. Michael's 4 base start
> codons, but also many start and stop codons are broken by introns.
> There is no reason not to use junctions.

Ah, ok - spaced on the distinction between codon/junction there

I'm still not comfortable with the hack to get round not having interbase
coordinates, where certain subgraphs of SOFA are treated as flanking bases
and the rest is treated as inclusive bases. I guess it's necessary for GFF
though.

should we make this explicit in the names; eg all types for features have
flanking-base coordinates have the suffix '_junction'?

> Richard
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