CDS tags....

Tim Cutts timc at chiark.greenend.org.uk
Tue Aug 29 08:18:03 EST 2000

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
>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!


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