[ssml] Redundancy in MSA for building HMM

[Kevin Karplus]

An HMM is a good way to model a domain family, but using HMMer without
calibration is likely to result in poor models.  You'll get better
models using the SAM package with the provided target2k script for
builing the multiple alignment, followed by the w0.5 script to do
appropriate thinning and sequence weighting for building a
superfamily-level model.  If you need to end up with a HMMer model,
you're still better off building the model with SAM and using
sam2hmmer.

If you don't pay careful attention to thinning and/or sequence
weighting, then models built from the usual redundant alignments are
terrible. 


------------------------------------------------------------
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, ISCB (starting Jan 2005)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Affiliations for identification only.