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. > >http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ >(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) >Effective Cycling Instructor #218-ck (lapsed) >Senior member, IEEE Board of Directors, ISCB (starting Jan 2005) >Professor of Biomolecular Engineering, University of California, Santa Cruz >Undergraduate and Graduate Director, Bioinformatics >Affiliations for identification only. >_______________________________________________ >ssml-general mailing list >ssml-general at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/ssml-general >