Re: [SO-devel] Question about CDS SO term (SO:0000316)

[Karen E. <kei...@ge...>]

Keith,
If we wanted to fix this without making people cry, we could add a term full_cds to be the whole thing. This would leave the split line cds the same.
But that will probably make a different set of people cry.
--K


On 9/30/11 2:48 PM, "Keith Bradnam" <krb...@uc...> wrote:

Hi,

I think you're right Karen, but Kevin's raised a good point. In a bacterial genome annotation (or in a single-exon eukaryotic gene), you could use one GFF line to represent an entire CDS sequence. This would be consistent with the SO definition. It strikes me that most GFF3 files are using 'CDS' to really represent what is more strictly a 'CDS segment' (a sequence that has a parent 'CDS'). I'm not sure whether the duality in how 'CDS' is currently used means that it is not going to be something that is easily changed (not without breaking lots of existing code and making grown bioinformaticians cry).

Regards,

Keith

P.S. Personally, I would like to see the addition of something like 'CDS_segment' as a new SO term to remove any confusion (apart from the confusion created by changing the status quo)

On Fri, Sep 30, 2011 at 1:41 PM, Karen Eilbeck <kei...@ge...> wrote:

Hi Kevin
I think that the mods use CDS as a split feature. So the total CDS of a transcript will have a start and stop, but the feature is across several lines of GFF3.
I could be wrong though...
--Karen

On 9/28/11 3:07 AM, "Kevin Howe" <kev...@wo... <http://kev...@wo...> > wrote:


Hi,

The definition of the "CDS" SO term states:

"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon."

Is this rather strict definition intentional? In the GFF3 specification, "CDS" is used to define an exonic region that is coding across its whole length (with population of the phase field compulsory).This usage is consistent with the majority of GFF3s I have come across.  Many (most) of these features will not start/end with start/stop coons.

So...is the definition of the term overly specific? Or are people using the term in an inappropriate context?

Many thanks,

Kevin Howe



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