[go] Putting method/program names into the with field for ISS

[Ben Hitz]

>
> I guess my question is, what excludes tRNA scan, and TMM predictors  
> from being RCA?
> and, if it is because they are sequence-based, will we need to  
> revisit this all over again when we have other predictions which  
> don't fit RCA or ISS in future?

If I understand Karen's position - it's that these methods rely more  
or less exclusively on "sequence and or structural" information.
And yet (IMHO), because they do not match a specific entity and/or  
family subfamily, they are clearly different types of "methods".

A possibly resolution might be to redefine ISS (and possibly rename)  
to specifically mean "homology based methods which match to a  
specific sequence entity or family".    This language has to be a bit  
vague to allow for homology assignments for RNAs.

tRNA scan /TMHMM would fall under RCA, and perhaps we should also  
adopt Karen's new code for "mixed computational analysis" for more  
integrative statistical methods.

Ben


--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu