[ssml] Redundancy in MSA for building HMM

[Dan Bolser]

On Wed, 6 Oct 2004, Kevin Karplus wrote:

>
>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

OK.

The thing is, sould you ever buid a model to find higly similar sequences,
or should you just use blast to do that?


>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.
>