CDS tags....

Ed Griffiths edgrif at sanger.ac.uk
Tue Aug 29 08:30:14 EST 2000


Ian,

> I don't really have any great feeling either way about in which coordinate set 
> the CDS description should be (although working in coordinates of what is 
> essentially a subsequence of a subsequence, while more correctly representing 
> the biology, is harder to get your head around).

Current concensus seems to favour having spliced-DNA coords.

> What I would like is to see this all properly implemented so that we can get 
> around the awful fudge that is prevalent now in the sanger human acedbs whereby 
> to describe the translated portion of a transcript two subsequence objects are 
> made, the transcript itself and then the translated (CDS) object.  To make this 
> look nice the views of the two objects are tweaked so that they are in different 
> colours and the translation lies on top.  

I don't see why we can't do this, it will require some changes to fmap code and
maybe a new tag, I'm not sure at the moment, but basically the code is all there
to do it.

> What seems nicer to me would be to only make transcript subsequences, and to 
> describe the translation of these using CDS Int Int in whatever coordinates are 
> deemed appropriate, and to add in a function to colour or fill in the translated 
> portion of the transcript in the fmap display.  (BTW I presume that the system 
> allows description of the translation of polycistronic messages?)

I don't see why we can't do this. My only doubts are that I don't know what
polycistronic means....

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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