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

[Benjamin Hitz]

Oh, then you were disagreeing with me too!  I think those should be  
RCA.  They are (in my mind) clearly distinct from "homologous pair or  
family" based methods such as Blast, Pfam, etc - and the distinction  
doesn't have to do with the type of information (I agree they all use  
sequence and/or structural information) used in creating a "link" but  
rather the WITH result of what the "match" is.

I find it very confusing to have ISS (PFam) WITH IPR:003939  and ISS  
(tRNAscan) WITH tRNAscan.  I suppose others (GOC and non-GOC) might  
be confused by ISS(Blast) WITH UniRef:P03930 as well!  But for  
whatever reason this confuses me less.


Ben
On Sep 11, 2007, at 11:42 AM, Gwinn-Giglio, Michelle wrote:

>
>
> Ben,
>
> Yes, sorry to not be clear - I was disagreeing with Val's  
> suggestion to use RCA for things like TMHMM and tRNAscan.  At least  
> I think that was Val's suggestion and that is what I diasagree with.
>
> Sorry to disagree with you Val.  :)
>
> Michelle
>
>
>
>
> -----Original Message-----
> From: Benjamin Hitz [mailto:hitz at genome.stanford.edu]
> Sent: Tue 9/11/2007 1:05 PM
> To: Gwinn-Giglio, Michelle
> Cc: GO mailing list
> Subject: Re: [go] Putting method/program names into the with field  
> for ISS
>
>
> On Sep 11, 2007, at 7:55 AM, Gwinn-Giglio, Michelle wrote:
>
> >
> >
> > Hi,
> >
> > I disagree.  I think taking this approach would significantly muddy
> > the waters in terms of distinguishing between ISS and RCA.
> >
> > Anything that is based only on sequence analysis, be it simple
> > Blast or vastly more complicated modeling methods, should be ISS
> > because at their heart they are all comparing sequences of known
> > function to ones with unknown function.  Whether they do simple
> > alignments to make that comparison or more complicated models, it
> > is still a sequence based analysis.
>
> I did not suggest otherwise.
>
> Ben
>
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO
> Consortium
> Stanford University ** hitz at genome.stanford.edu
>
>
>
>
>

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



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