[ssml] HMM

Kevin Karplus karplus at soe.ucsc.edu
Tue Jan 6 16:02:30 EST 2004


Null models are important for scoring and for doing local, rather than
global alignment.  You can see the local/global thing in 

@article{bucher-karplus,
	title="A Flexible Motif Search Technique based on Generalized Profiles",
	author="Philipp Bucher and Kevin Karplus and Nicolas Moeri and
	Kay Hoffman",
	journal="Computers and Chemistry",
        year="1996",
        month=Jan,
	volume="20", number="1", pages="3--24"
}


There are several papers on null models for scoring, many with Richard
Hughey as one of the authors.

I'm going to be resubmitting a revised paper on reverse-sequence null
models soon.  (The referees had some excellent suggestions that took a
few months to implement and test, using student labor.  It turned out
that their ideas were wrong, but the testing needed to be done to show
it.)







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