Best Library For Profile Hmm'S

Question

[Stephen Olsen]

I'm looking to train a profile HMM to try and recognize different domains in a protean sequence. I'm sure there are library's to do this and was wondering what the best one to use would be. I'd prefer something in python or with python bindings. Thanks

Answer 1

[Rm]

Pfam, TIGRfam, Superfamily, Smart....

The Pfam database is one the most important collections of information in the world for classifying proteins. The database categorises 75 per cent of known proteins to form a library of protein families - a 'periodic table' of biology.

TIGRFAMs are protein families based on Hidden Markov Models or HMMs

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments 1. Julian Gough* and 2. Cyrus Chothia

http://supfam.org/SUPERFAMILY/

Even SMART use protein domain HMMs

Editing to Add Python HMM modules

Ghmm http://ghmm.sourceforge.net/ghmm-python-tutorial.html

Hmmus has some C implementations of HMM algorithms with Python bindings http://pypi.python.org/pypi/hmmus/0.2.16

Sarment: Python modules for HMM analysis and partitioning of sequences http://bioinformatics.oxfordjournals.org/content/21/16/3427.full

Answer 2

[Khader Shameer]

You may try the Pfam database for the HMM of 11912 protein domain families. You can download the HMM profile for the current release from the Pfam FTP: Pfam-A.hmm.gz. You may use HMMER3 for searches or to analyze the Pfam based HMMs.