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

[Jim Hu]

On Sep 20, 2007, at 11:16 AM, Karen Christie wrote:

> <snip>
>> It seem that RCA has not been considered, because most of the  
>> function predictions using RCA so far have some experimental  
>> component (In fact the RCA code says non-sequence-based  
>> computational method).
>
> I think we did consider RCA for tRNAscan and snoRNAs (at the 2006  
> Annot Camp), but then rejected it at the Jan 2007 GO meeting in  
> response to Michelle Gwinn's argument that everything based purely  
> on analysis of the sequence of the gene product should be ISS, even  
> if multiple types of sequence analysis were combined.
>
> While it is true that the original RCA documentation did say non- 
> sequence based method, at the St. Croix meeting, Sue Rhee brought  
> up the point about analyses that combined non-sequence and sequence  
> based data and we agreed that these could be RCA. Thus in the draft  
> document, I've made a new section called ICA with proposed  
> guidelines that I think are more in line with the idea that these  
> analyses involve multiple data sets or even multiple kinds of data  
> sets.
>
> http://www-dev.yeastgenome.org/draftGO/go/www/GO.evidence.new.shtml
>

I know that I probably missed this being brought up many times in the  
past, but as a newbie, when I see ISS, I key in on Sequence  
Similarity not just Sequence.   I think that biologists seeing this  
read it as a way of saying inferred from evolutionary relationship  
which is itself inferred from the sequence similarity with X.  I  
don't think of similarity of statistical profiles of periodic amino  
acid content.

So, while I'm not that familiar with the specifics of the programs,  
it seems to me that profile HMMs are very different from TMHMM.  If  
the protein folders get to the holy grail of predicting structure/ 
function from sequence based on chemistry, I would not call that an  
ISS, even though the sequence is the key input.

I see where the RCA documentation doesn't fit with my view.  But it  
seems to me that the fundamental thing you want to distinguish is the  
inferences that are based on evolution/common descent and those that  
are not. I would use ISS for the former and RCA for everything else.

Jim

<snip>
=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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