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

[Gwinn-Giglio, Michelle]

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




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