The DOI matches its Crossref record; 21 of the 30 references it cites were found in a registry or an index.
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 (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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UniProt: the Universal Protein knowledgebase
Apweiler, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,593
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
Self-citationThe Pfam protein families database: towards a more sustainable future
Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., Sangrador-Vegas, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1344 · Cited by 5,975
Self-citationHMMER web server: interactive sequence similarity searching
Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952
Self-citationEddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515
Self-citationZerbino, D. R., Achuthan, P., Akanni, W., Amode, M. R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C. G., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1098 · Cited by 2,605
UniProt: the universal protein knowledgebase
The UniProt Consortium (2018) · Nucleic Acids Research · doi:10.1093/nar/gky092 · Cited by 2,043
Rawlings, N. D., Barrett, A. J., Thomas, P. D., Huang, X., Bateman, A., & Finn, R. D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1134 · Cited by 1,749
Self-citationInterPro in 2017—beyond protein family and domain annotations
Finn, R. D., Attwood, T. K., Babbitt, P. C., Bateman, A. G., Peer Bork, B., Bridge, A. J., Chang, H.-Y., Dosztányi, Z., El-Gebali, S., Fraser, M., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1107 · Cited by 1,455
Self-citationFinn, R. D., Clements, J., Arndt, W. D., Miller, B. L., Wheeler, T. J., Schreiber, F., Bateman, A. G., & Eddy, S. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv397 · Cited by 911
Self-citationTIGRFAMs and Genome Properties in 2013
Haft, D. H., Selengut, J., Richter, R. A., Harkins, D. M., Basu, M. K., & Beck, E. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1234 · Cited by 579
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
Kersey, P. J., Allen, J. E., Allot, A., Barba, M., Boddu, S., Bolt, B. J., Carvalho‐Silva, D., Christensen, M. B., Davis, P. A., Grabmüller, C., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1011 · Cited by 448
Self-citationCATH: an expanded resource to predict protein function through structure and sequence
Dawson, N. L., Lewis, T. E., Das, S., Lees, J., Lee, D., Ashford, P., Orengo, C. A., & Sillitoe, I. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1098 · Cited by 381
Predicting active site residue annotations in the Pfam database
Mistry, J., Bateman, A. G., & FINN, R. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-298 · Cited by 299
Self-citationPIRSF: family classification system at the Protein Information Resource
Wu, C. H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh097 · Cited by 249
Mitchell, A., Scheremetjew, M., Denise, H., Potter, S., Tarkowska, A., Qureshi, M., Salazar, G. A., Pesseat, S., Boland, M. A., Hunter, F. M. I., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx967 · Cited by 213
Self-citationThe HMMER Web Server for Protein Sequence Similarity Search
Prakash, A., Jeffryes, M., Bateman, A. G., & Finn, R. D. (2017) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.40 · Cited by 212
Self-citationTreeFam v9: a new website, more species and orthology-on-the-fly
Schreiber, F., Patrício, M., Muffato, M., Pignatelli, M., & Bateman, A. G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1055 · Cited by 149
Chen, C., Natale, D. A., Finn, R. D., Huang, H., Zhang, J., Wu, C. H., & Mazumder, R. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018910 · Cited by 101
Self-citationThe SUPERFAMILY 1.75 database in 2014: a doubling of data
Oates, M. E., Stahlhacke, J., Vavoulis, D. V., Smithers, B., Rackham, O. J. L., Sardar, A. J., Zaucha, J. M., Thurlby, N., Fang, H., & Gough, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1041 · Cited by 87
The EBI search engine: EBI search as a service—making biological data accessible for all
Park, Y. M., Squizzato, S., Buso, N., Gur, T., & Lopez, R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx359 · Cited by 33
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9 of the 30 references couldn’t be matched to a known paper.
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Evolutionary-scale prediction of atomic level protein structure with a language model
Lin, Z., Akin, H., Rao, R., Hie, B., Zhu, Z., Lu, W., Smetanin, N., Verkuil, R., Kabeli, O., Shmueli, Y., et al. (2022) · doi:10.1101/2022.07.20.500902 · Cited by 5,990
The EMBL-EBI search and sequence analysis tools APIs in 2019
Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz268 · Cited by 4,167
Self-citationImproved protein structure prediction using predicted interresidue orientations
Yang, J., Anishchenko, I., Park, H., Peng, Z., Ovchinnikov, S., & Baker, D. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1914677117 · Cited by 1,421
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P., Bridge, A., Brown, S. D., Chang, H.-Y., El-Gebali, S., Fraser, M. I., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1100 · Cited by 1,426
Self-citationProtein Sequence Analysis Using the MPI Bioinformatics Toolkit
Gabler, F., Nam, S., Till, S., Mirdita, M., Steinegger, M., Söding, J., Lupas, A. N., & Alva, V. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.108 · Cited by 831
Metadata
- 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
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