IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

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
>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.








More information about the Acedb mailing list

Send comments to us at archive@iubioarchive.bio.net