HMMER web server: 2018 update
Open accessAbstract
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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MGnify sequence MGYP000936678158 has no significant sequence matches to any entry in UniRef90, nor any significant matches via a jackhmmer reference proteome search, but has a predicted structure conserved across many nucleases (PDB 5YET B, TM-score 0.68; PDB 3HR4 A, TM-score 0.67).
“MGnify sequence MGYP000936678158 has no significant sequence matches to any entry in UniRef90, nor any significant matches via a jackhmmer (47) reference proteome search, but has a predicted structure conserved across many nucleases (PDB 5YET B, TM-score 0.68; PDB 3HR4 A, TM-score 0.67)”
From Evolutionary-scale prediction of atomic level protein structure with a language model (2022) · cites this paper as [47]
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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
- 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
- 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
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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