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
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bti629
------------------------------------------------------------
Kevin Karplus karplus at soe.ucsc.eduhttp://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)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Affiliations for identification only.