Profile Hidden Markov Models

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 1999 Jan 27

PMID 9918945

Citations 2326

Authors

S R Eddy

Affiliations

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Abstract

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.

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