Fwd: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + PeptidePropertyType Table

[Chris S. <sto...@SN...>]

Hi Folks,
Jessie Kissinger has set up gusdev at the University of Georgia and I 
hope that she will be joining these discussions soon. As you can see 
from her mail below, there are issues she needs to address that we've 
been trying to avoid. Sigh. It may be time to address them.

Cheers,
Chris


Begin forwarded message:

> 	We are still setting up so, needless to say, we have not made a 
> detailed walk through the schema and the features of every table yet. 
> We have made a list of a few concepts that we presume will need to be 
> added to the schema to accomplish some of our goals and many of these 
> will also be needed by Sanger since they are particular to 
> Kinetoplastid organisms and or the sequencing strategy.
>
> 	Some issues that are on my list are the following:
>
> 1 - The concept of a homologous chromosome. T. cruzi is being 
> sequenced as a diploid.
>
> 2 - The concept of multiple genes per transcript, kinetoplastid 
> organisms are eukaryotic but use polycistronic transcription. This 
> feature is commonly ignored, but now that we have expression studies, 
> we need to be able to study expression levels of genes on the same 
> transcript to get testable ideas about post-transcription mechanisms 
> of control.
>
> 3 - The concept of a 5' splice leader sequence (the idea that it 
> exists and keeping track of which leader it was, there are multiple 
> leaders).  Currently, nobody keeps track of this, they just remove it 
> and analyze the rest.
>
> 4 - Kinetoplastid mitochondria a quite weird, they consist of mini and 
> maxi circle plasmid DNA's and heavily utilize RNA editing. Thus in 
> addition to the keeping track of mini and maxi circle DNA's we need 
> the concept of a guide RNA and an 'edited' site in a message that is 
> edited.  Idealy one would like to record the nature of the edit, i.e. 
> what change is made, what nucleotides are added to the sequence.  
> Transcripts can only encode ORF's after they have been edited.