Profile hidden Markov models
Open accessAbstract
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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References 68 · Cited by 5,515
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- Authors
- Eddy, S. R.
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- Eddy, S R
- ORCID
- Eddy, S R
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 1998-01-01
- Volume
- 14
- Issue
- 9
- Pages
- 755-763
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2151831732
- Cited by
- 5,515
- References
- 68
- Citations by year
- 2026: 98 · 2025: 152 · 2024: 218 · 2023: 193 · 2022: 247 · 2021: 342 · 2020: 237 · 2019: 227 · 2018: 232 · 2017: 192 · 2016: 212 · 2015: 175 · 2014: 191 · 2013: 235 · 2012: 250
- FWCI
- 2.73
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Eli Lilly and Company
- University of California, Santa Cruz
- National Institutes of Health
- National Human Genome Research Institute (HG01363, R01HG001363, R01-HG01363)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- profile hidden Markov models, multiple sequence alignment, position weight matrices, remote homology detection, protein structure prediction, sequence database searching
- MeSH terms
- Humans, Markov Chains, Software, Sequence Alignment, Peptide Library
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