Cited by 5,952Genomics and Phylogenetic StudiesMachine Learning in BioinformaticsAlgorithms and Data Compression

HMMER web server: interactive sequence similarity searching

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Finn, R. D., Clements, J., Eddy, S. R.·2011·Nucleic Acids Research

Abstract

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.

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Authors
Finn, R. D., Clements, J., & Eddy, S. R.
Affiliations
Howard Hughes Medical Institute (US)
Corresponding author
Finn, R. D.
Venue
Nucleic Acids Research
Published
2011-05-18
Volume
39
Issue
suppl
Pages
W29-W37
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
OpenAlex
W2135621733
Cited by
5,952
References
22
Citations by year
2026: 416 · 2025: 560 · 2024: 576 · 2023: 519 · 2022: 607 · 2021: 610 · 2020: 437 · 2019: 375 · 2018: 337 · 2017: 339 · 2016: 316 · 2015: 322 · 2014: 242 · 2013: 184 · 2012: 93
FWCI
68.75
Type
journal article
Language
en
Open access
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
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
  • Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
Keywords
profile hidden Markov models, Pfam, multiple sequence alignment, REST API, batch query processing, search result visualization, protein database searching
MeSH terms
Software, Sequence Alignment, Internet, Sequence Analysis, Protein

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