CDS tags.... bionet-software-acedb@net.bio.net, edgrif@sanger.ac.uk, informaticsg@sanger.ac.uk

id1 at sanger.ac.uk id1 at sanger.ac.uk
Tue Aug 29 08:18:13 EST 2000

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).

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.  

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 believe that this must be what was originally intended but it isn't getting 
used like this in the human databases at least.  


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