CDS tags....

Ed Griffiths edgrif at sanger.ac.uk
Fri Aug 25 06:48:32 EST 2000


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:

           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                      |

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