CDS tags....

James Gilbert jgrg at sanger.ac.uk
Fri Aug 25 10:37:54 EST 2000



Changing to unspliced coordinates would be a good
plan as far as I'm concerned.

	James

On Fri, 25 Aug 2000, Ed Griffiths wrote:

> All,
> 
> In fixing a couple of bugs to do with protein display from xace I came across an
> inconsistency that would be worth fixing:
> 
> If you are looking at some sequence object such as a supported CDS, then it will
> have a series of exons specified something like this:
> 
> 
> Structure From Source bA404F10
>                Source_Exons 1  82
>                             26575 26877
>                             30296 30562
> 
> 
> The model/code allows you to specify the CDS start/end within the source_exons:
> 
> Properties
>            Coding CDS <start> <end>
> 
> BUT currently the start/end values must be specified in the coordinate system
> of the spliced dna, not the above coordinate system. If you specified 30500 as
> the coordinate where you wanted the coding to stop you would get a surprise as
> this will lead the protein display window to display vast numbers of 'X's where
> it has run off the end of the spliced DNA, in the above example the spliced DNA
> is only 652 long....
> 
> It would make more sense to me if you could specify a start/end in the
> coordinate frame of the Source_Exons and then the code did the translation to
> the spliced dna.
> 
> I don't want to make this change however until I've got your opinions on it
> because I know that people often store values in acedb that they later extract
> via ace dumps and perl script filtering and I don't want to mess that up.
> 
> Pleass send me a note if you have an opinion on this...
> 
> cheers Ed
> 
> p.s. please restrict yourself to this very specific problem, if you think the
> model should all be completely different, that's a separate matter. (I don't
> want to stifle discussion, but I don't want to start off a landslide of
> discussion either...) 
> 
>  ------------------------------------------------------------------------
> | 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                      |
>  ------------------------------------------------------------------------
> 

James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919








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