In article <200008290836.JAA28727 at griffin.sanger.ac.uk>,
Richard Durbin <rd at sanger.ac.uk> wrote:
>> BUT currently the start/end values must be specified in the coordinate system
>> of the spliced dna, not the above coordinate system.
>>This was intentional. In fact it is more work to do it this way than by
>specifying
>start/end in the coordinate frame of the Source_Exons. The principle is that
>coordinates in an acedb sequence object should be with respect to the
>DNA that is
>represented by the object. In my view, the Source_exons information is in the
>wrong place (should be in the parent, or done with Exon/Intron objects),
>but that
>is another story, as Ed says.
I agree. The ideal solution would be distinct intron-exon objects
(which could then, perhaps, be shared by transcripts, which would
probably give a clearer picture of alternative splicing).
As it is, I'd rather keep the spliced coordinates. I do a lot of
processing with CDSs in perl, and once I've constructed the mRNA using
the Source_Exon values, finding the CDS sequence is trivial using
spliced coordinates. Leave it the way it is, Ed!
Tim.
