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      Profile hidden Markov models.

      Bioinformatics

      Humans, Markov Chains, Peptide Library, Sequence Alignment, methods, Software

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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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          Journal
          9918945

          Chemistry

          Humans, Markov Chains, Peptide Library, Sequence Alignment, methods, Software

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