[ssml] HMM fro SCOP domain families.

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Mon Sep 27 14:15:12 EDT 2004

On Mon, 27 Sep 2004, Kevin Karplus wrote:

>Goel, Manisha wrote
>> Is there any ready source of getting the HMM profile for SCOP domain
>> families ?
>Yes, that is the SUPERFAM family of HMM models.
>(or http://supfam.org )

These HMM models are 'labeled' with the SCOP superfamily from which they
were derived, although they may or may not be SCOP family specific.

Natrually a HMM built from seed sequences in one family can produce
significant hits to sequences in other families within the superfamily.
However, it is not always that case that a single 'superfamily' model
produces good hits to every family in a superfamily.

A design feature of the superfamily library is that it provides many
models for one superfamily (starting from many non-redundant seed
sequences), allowing good overall coverage of all the (known) families in
that superfamily. The problem is that the results can be difficult to
interpret back at the family level.

>Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
>life member (LAB, Adventure Cycling, American Youth Hostels)
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>Senior member, IEEE	Board of Directors, ISCB (starting Jan 2005)
>Professor of Biomolecular Engineering, University of California, Santa Cruz
>Undergraduate and Graduate Director, Bioinformatics
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