Profile hidden Markov models.
SR Eddy�- Bioinformatics (Oxford, England), 1998 - academic.oup.com
Bioinformatics (Oxford, England), 1998•academic.oup.com
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�…
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�…
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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