Bioinformatics, Vol 14, 755-763, Copyright © 1998 by Oxford University Press
SR Eddy
The recent literature on profile hidden Markov model (profile HMM) methods
and software is reviewed. Profile HMMs turn a multiple sequence alignment
into a position-specific scoring system suitable for searching databases
for remotely homologous sequences. Profile HMM analyses complement standard
pairwise comparison methods for large- scale sequence analysis. Several
software implementations and two large libraries of profile HMMs of common
protein domains are available. HMM methods performed comparably to
threading methods in the CASP2 structure prediction exercise.
ARTICLES
Profile hidden Markov models
Department of Genetics, Washington University School of Medicine, 4566 Scott Avenue, St Louis, MO 63110, USA. eddy@genetics.wustl.edu
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