Cited by 2,607Genomics and Phylogenetic StudiesMachine Learning in BioinformaticsScientific Computing and Data Management

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HMMER web server: 2018 update

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Potter, Simon C, Luciani, Aurélien, Eddy, Sean R, Park, Youngmi, Lopez, Rodrigo, Finn, Robert D·2018·Nucleic Acids Research

DOI 10.1093/nar/gky448PMC PMC6030962

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Abstract

The HMMER webserver [http://www.ebi.ac.uk/Tools/hmmer] is a free-to-use service which provides fast searches against widely used sequence databases and profile hidden Markov model (HMM) libraries using the HMMER software suite (http://hmmer.org). The results of a sequence search may be summarized in a number of ways, allowing users to view and filter the significant hits by domain architecture or taxonomy. For large scale usage, we provide an application programmatic interface (API) which has been expanded in scope, such that all result presentations are available via both HTML and API. Furthermore, we have refactored our JavaScript visualization library to provide standalone components for different result representations. These consume the aforementioned API and can be integrated into third-party websites. The range of databases that can be searched against has been expanded, adding four sequence datasets (12 in total) and one profile HMM library (6 in total). To help users explore the biological context of their results, and to discover new data resources, search results are now supplemented with cross references to other EMBL-EBI databases.

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Authors: Potter, S. C., Luciani, A., Eddy, S. R., Park, Y., Lopez, R., & Finn, R. D.
Affiliations: European Bioinformatics Institute (GB)
Howard Hughes Medical Institute (US)
EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Corresponding author: Finn, Robert D
ORCID: Potter, Simon C
Luciani, Aurélien
Eddy, Sean R
Finn, Robert D
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2018-06-14
Volume: 46
Issue: W1
Pages: W200-W204
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gky448
PMC: PMC6030962
OpenAlex: W2918063357
Cited by: 2,607
References: 30
Citations by year: 2026: 348 · 2025: 433 · 2024: 407 · 2023: 385 · 2022: 372 · 2021: 357 · 2020: 208 · 2019: 88 · 2018: 9
FWCI: 61.61
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/4.0/ (vor)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
Funders: Howard Hughes Medical Institute (R01 HG009116)
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
Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
Keywords: profile hidden Markov models, sequence database searching, domain architecture, sequence databases
MeSH terms: Markov Chains, Software, User-Computer Interface, Sequence Analysis, Catalytic Domain, Internet, Sequence Analysis, Protein, Databases, Genetic

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