CDS tags....

Ed Griffiths edgrif at sanger.ac.uk
Tue Aug 29 08:30:24 EST 2000


Tim,

> 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).

OK, I think everyone would like to see this...

> 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!

Let me emphasise that no change has been made to the coordinate frame for the
CDSs, its all just as it was...

What I have done is fix a bug whereby, for reverse strand CDS objects, if you
wished to specify a start position, you were forced to specify both the start
and end positions of the CDS before the fmap code recognised the new start
position. This fix is in Augusts build.

cheers Ed

 ------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group,                    |
|               The Sanger Centre, Wellcome Trust Genome Campus,         |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk   URL: http://www.sanger.ac.uk/Users/edgrif |
|   Tel: +44-1223-494780       Fax: +44 1223 494919                      |
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