[Bioperl-l] COG software?

[Rick Westerman]

Paul Gordon wrote:

 >Provided you have the computational power...
 >What I've found very useful is taking the MSAs provided by NCBI and
 >creating an HMM library.

     That is a good idea.  Computer power I have or can find somewhere.

     Using HMMs gets rid of "coginator's" idea of matching X number of 
clades in order to have a significant match.  That may not be a bad thing, 
though, since it requires less parsing; i.e., with an HMM the COG is either 
there or not there while with Blast a person/program would have to count 
the number of matches.  Granted not hard but just a bit more coding 
involved.  And every time I think of coding a little then I get caught up 
in feature creep. :-(

Thanks,



-- Rick

Rick Westerman
westerman@purdue.edu

Phone: (765) 494-0505                         FAX: (765) 496-7255
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Bioinformatics specialist at the Genomics Initiative.
Part time system manager of Biochemistry department.

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