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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Figure 1. Results of a search in the ‘score’ view with the new ‘Cross references’ column, populated with links to the hit sequence in other EMBL-EBI databases. As the page is loaded, these symbols may disappear if no cross-references are found in this category.CC BY-NC · PubMed Central

Figure 2. New taxonomy view. The tree is navigable via keyboard or mouse, with the red circle showing the currently selected node, and the size of the blue circles being proportional to the number of hits. Figure 3. As the user changes the selected node, the red line highlights the selected route to the node. The lineage is shown below the figure and the small barchart shows the distribution of E-values at the selected node.CC BY-NC · PubMed Central

Figure 3. Annotation of the domain graphic with the catalytic active sites predicted by Pfam, with extra information about the middle site displayed in a mouse-activated pop-up.CC BY-NC · PubMed Central

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A chromosome‐level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination
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Comparative analysis of the complete chloroplast genome of seven Nymphaea species
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Discovery and genetic characterization of a novel orthonairovirus in Ixodes ricinus ticks from Danube Delta
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Identification and Characterization of Cinnamyl Alcohol Dehydrogenase Encoding Genes Involved in Lignin Biosynthesis and Resistance to Verticillium dahliae in Upland Cotton (Gossypium hirsutum L.)
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Identification and mechanism characterization of Streptomyces griseoaurantiacus XQ-29 with biocontrol ability against pepper southern blight caused by Sclerotium rolfsii
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The type V effectors for CRISPR/Cas-mediated genome engineering in plants
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Structure‐aware deep learning model for peptide toxicity prediction
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“…that have been applied on this dataset include BLAST (Altschul, 1997), BLAST-score (Altschul, 1997), InterProScan (Quevillon et al., 2005), HmmSearch (Potter et al., 2018), ClanTox (Naamati et al., 2009), ToxinPred (Gupta et al., 2013), ToxDL (Pan et al., 2021), and ToxIBTL (Wei et al., 2022).”
BackgroundMethod
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A chromosome‐level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology
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“Finally, DNA and protein homologs are identified using NCBI BLASTp ( 33 ) and HMMER3 ( 34 ) in the BLASTp and HMMER search tools.”
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“We aligned a randomly selected 1,000 singleton clusters against the representative sequences of non-singleton clusters (i.e., those containing ≥ 2 sequences) using SWIPE with the following parameters: -a 18 -m '8 std qcovs' -p 1.”
Method
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TcMYC2 regulates Pyrethrin biosynthesis in Tanacetum cinerariifolium
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VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
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Self-citation
Genome-wide investigation of bHLH genes and expression analysis under salt and hormonal treatments in Andrographis paniculata
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Comparative mucomic analysis of three functionally distinct Cornu aspersum Secretions
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How do bacterial endosymbionts work with so few genes?
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“Gene presence and absence were calculated from a combination of literature review, existing GenBank annotations, and by performing searches against HMMER [12] profiles in the Pfam and TIGRFAM databases.”
Method

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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