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[Computational-biology] Re: Point Specific Mutation Matrix vs. profile HMM ?

Kevin Karplus karplus at cheep.cse.ucsc.edu
Mon Feb 13 19:40:43 EST 2006

On 2006-02-12, Michael Spitzer <professa at gmx.net> wrote:

> The main (and only?) disadvantages
> of profile HMMs seem to be higher computational cost and a less solid
> statistical theory corresponding to E-value calculation, compared to
> PSI-BLAST. The latter may have changed by now, but I'm not aware of
> current publications on this at the moment.

Look at

Kevin Karplus, Rachel Karchin, George Shackleford, and Richard
Hughey. Calibrating E-values for hidden Markov models with
reverse-sequence null models. 

Bioinformatics 2005 21(22):4107-4115; doi:10.1093/bioinformatics/bti629 


Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors & Chair of Education Committee, ISCB)
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Effective Cycling Instructor #218-ck (lapsed)
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