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

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 access

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

Open this paper in CoChat — free account Open PDF

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/nar/gky448

Cites

21 of 21 references verified0 citation errors · 0 not checkable

Statistics

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

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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-citation
The 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-citation
HMMER 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-citation
Profile hidden Markov models
Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515
Self-citation
Ensembl 2018
Zerbino, 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
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database
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-citation
InterPro 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-citation
HMMER web server: 2015 update
Finn, 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-citation

Show all 30 references

Sorted by citations

Items 901–1,000 of 1,002

Genomic-Wide Identification and Characterization of the Uridine Diphosphate Glycosyltransferase Family in Eucommia ulmoides Oliver
Ouyang, D., Wang, L.-C., Tang, T., & Feng, H. (2021) · Plants · doi:10.3390/plants10091934 · Cited by 11
PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders
Manso, J. A., Marcos, T. K., Ruiz‐Martín, V., Casas, J., Alcón, P., Crespo, M. S., Bayón, Y., de Pereda, J. M., & Alonso, A. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-022-04173-w · Cited by 12
Genome-Wide Identification and Expression Profiles of C-Repeat Binding Factor Transcription Factors in Betula platyphylla under Abiotic Stress
Zhang, X., Yu, J., Wang, R., Liu, W., Chen, S., Wang, Y., Yu, Y., Qu, G., & Chen, S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241310573 · Cited by 11
Analysis of a Mad2 homolog in Trypanosoma brucei provides possible hints on the origin of the spindle checkpointPreprint
Akiyoshi, B. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.29.424754 · Cited by 11
Comprehensive identification and analysis of clusters of tandemly duplicated genes reveal their contributions to adaptive evolution of green plants
Yang, Y., Li, Q., Li, H., Qi, K., Xie, Z., Wang, Z., Zou, Y., Huang, B., Hu, J., Qiao, X., et al. (2025) · The Plant Journal · doi:10.1111/tpj.70370 · Cited by 11
Genetic basis of phytoalexin-mediated chemical defense in plants
Wang, Z., Han, L., Gao, L., Zhang, L., Xie, Y. D., Liu, H., Fan, J., Wu, M., Yue, N., Wang, Y., et al. (2026) · Cell · doi:10.1016/j.cell.2026.04.021 · Cited by 10
MyCLADE: a multi-source domain annotation server for sequence functional exploration
Vicedomini, R., Blachon, C., Oteri, F., & Carbone, A. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab395 · Cited by 10
Genome-wide identification and characterization of F-box family proteins in sweet potato and its expression analysis under abiotic stress
Amoanimaa‐Dede, H., Shao, Z., Su, C., Yeboah, A., & Zhu, H. (2022) · Gene · doi:10.1016/j.gene.2022.146191 · Cited by 10
The embryonic transcriptome of Parhyale hawaiensis reveals different dynamics of microRNAs and mRNAs during the maternal-zygotic transition
Calvo, L., Birgaoanu, M., Pettini, T., Ronshaugen, M., & Griffiths‐Jones, S. (2022) · Scientific Reports · doi:10.1038/s41598-021-03642-9 · Cited by 10
Novel strain of Pseudoruminococcus massiliensis possesses traits important in gut adaptation and host-microbe interactions
Hiippala, K., Khan, I., Ronkainen, A., Boulund, F., Vähä-Mäkilä, H., Suutarinen, M., Seifert, M., Engstrand, L. G., & Satokari, R. M. (2021) · Gut Microbes · doi:10.1080/19490976.2021.2013761 · Cited by 11
Interface engineering of cellobiose dehydrogenase improves interdomain electron transfer
Reichhart, T. M. B., Scheiblbrandner, S., Sygmund, C., Harreither, W., Schenkenfelder, J., Schulz, C., Felice, A. K. G., Gorton, L. G. O., & Ludwig, R. (2023) · Protein Science · doi:10.1002/pro.4702 · Cited by 10
Propeptide-Mediated Allosteric Regulation of Xylanase Xyl-1: An Integrated Experimental and Computational Analysis
Wu, Y. F., Chen, K.-W., Li, Y., Qiu, K., Lu, G., Shu, T., Sun, T., Hou, Z., Wu, Y., & Yu, L. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c03431 · Cited by 10
Exploring the extensin gene family: an updated genome-wide survey in plants and algae
Cheng, S., Chu, P.-K., Chen, Y.-J., Wu, Y.-H., & Huang, M. (2023) · Journal of Experimental Botany · doi:10.1093/jxb/erad380 · Cited by 10
Transcriptomics and metabolomics of blood, urine and ovarian follicular fluid of yak at induced estrus stage
Zhao, H., Huang, Y., Shu, S., Wang, G., Fu, C., Huang, R. S., Zhang, J., Su, H., He, Y., Lei, C., et al. (2024) · BMC Genomics · doi:10.1186/s12864-024-10079-7 · Cited by 10
Genome-Wide Identification and Expression Analysis of the DMP and MTL Genes in Sweetpotato (Ipomoea batatas L.)
Pan, Z., Li, Z., Han, Y., & Sun, J. (2024) · Genes · doi:10.3390/genes15030354 · Cited by 10
Parasitic dodder expresses an arsenal of secreted cellulases with multi-substrate specificity during host invasion
Edema, H., Bawin, T. G. A., Olsen, S., Krause, K., & Karppinen, K. (2024) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2024.108633 · Cited by 10
Genome-wide identification and stress response analysis of BcaCPK gene family in amphidiploid Brassica carinata
Zuo, D., Lei, S., Qian, F., Gu, L., Wang, H., Du, X., Zeng, T., & Zhu, B. (2024) · BMC Plant Biology · doi:10.1186/s12870-024-05004-9 · Cited by 10
“…protein sequence was used to perform a local blast against the B. carinata genome data (http://brassicadB.org/brad/) [46], with an E value threshold of 1e-5; (2) The sequences containing both the EF-hand motif and Pkinase domain were screened using HMMER 3.0 software [47], with domE value of 1e-5.”
MethodInfluential
Identification of tomato F-box proteins functioning in phenylpropanoid metabolism
Shin, D., Cho, K. H., Tucker, E., Yoo, C. Y., & Kim, J. (2024) · Plant Molecular Biology · doi:10.1007/s11103-024-01483-4 · Cited by 11
“0 annotation) (Tomato Genome Consortium 2012) et al. 2015; Potter et al. 2018).”
EBI Search: providing discovery tools for biological metadata in 2025
Pearce, M. B. Y. D. J., Basutkar, P., Neto, R. C. J., Subramoniam, V. V., Neis, K., Tutis, I., & Hermjakob, H. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf359 · Cited by 10
“Some data resources have been deprecated, including HMMER [ 15 ].”
Comparative genomics of three medicinal Glycyrrhiza species unveiled novel candidates for the production of important bioactive compounds
Li, Y., Xia, C., Luo, M., Huang, Y., Xia, Z., Li, Y., & Wang, Y. (2025) · The Plant Journal · doi:10.1111/tpj.70223 · Cited by 10
Growth physiology, genomics, and proteomics of Desulfurivibrio dismutans sp. nov., an obligately chemolithoautotrophic, sulfur disproportionating and ammonifying haloalkaliphile from soda lakes
Sorokin, D., Merkel, A., Ziganshin, R., & Kublanov, I. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1590477 · Cited by 12
Genome-wide identification and salt stress-responsive expression profiling of Aux/IAA gene family in Asparagus officinalis
Wen, S., Ying, J., Ye, Y., Cai, Y., Li, L., & Qian, R. (2025) · BMC Plant Biology · doi:10.1186/s12870-025-06780-8 · Cited by 10
“Candidate AoIAA gene family members were identified using the Hidden Markov Model (HMM) file of the conserved Aux/IAA domain (PF02309) from the Pfam database (http://pfam.xfam.org/) [59, 60].”
Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants
Tang, Y., Zhan, P.-C., Wu, Y., Zhang, T., Yin, D., Gao, Y., Yu, Y., Qiu, S., Zhao, J., Zhang, X., et al. (2025) · Microbiome · doi:10.1186/s40168-025-02139-1 · Cited by 10
Gymnosperm-specific CYP90Js enable biflavonoid biosynthesis and microbial production of amentoflavone
Dai, X.-H., Zhu, J.-M., Wang, G., Ren, Y., Liu, H., & Wang, Y. (2025) · Nature Communications · doi:10.1038/s41467-025-62990-6 · Cited by 11
Structural and evolutionary determinants of Argonaute function
Wallmann, A., & de Pette, M. V. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf962 · Cited by 9
“With this initial alignment, the profile-based JACKHMMER [ 46 ] was used to search the entire UniprotKB database [ 47 ] with a significance E-value cutoff of 0.01 (Sequence), 0.03 (Hit), and 5 iterations.”
Influential
A conserved adaptor orchestrates co-secretion of synergistic type VI effectors in gut Bacteroidota
Li, W., Zheng, S., Xu, X., He, J. J., Jiao, X., Wang, M., Hu, W. S., Li, S., Jiang, X., Lim, B., et al. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.09.012 · Cited by 10
VdNop12 , containing two tandem RNA recognition motif domains, is a crucial factor for pathogenicity and cold adaption in Verticillium dahliae
Zhang, J., Cui, W., Haseeb, H. A., & Guo, W. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15268 · Cited by 10
Genome-wide identification and evolution of HECT genes in wheat
Meng, X., Yang, T., Liu, J., Zhao, M., & Wang, J. (2020) · PeerJ · doi:10.7717/peerj.10457 · Cited by 11
Genome-Wide Identification of the Early Flowering 4 (ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance
Tian, M., Wu, A., Zhang, M., Zhang, J., Wei, H., Yang, X., Ma, L., Lü, J., Fu, X., Wang, H., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.686852 · Cited by 10
Phenylpropanoid Biosynthesis Gene Expression Precedes Lignin Accumulation During Shoot Development in Lowland and Upland Switchgrass Genotypes
Saha, P., Lin, F., Thibivilliers, S., Xiong, Y., Pan, C., & Bartley, L. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.640930 · Cited by 10
Genome-wide identification and analysis of HECT E3 ubiquitin ligase gene family in Ruditapes philippinarum and their involvement in the response to heat stress and Vibrio anguillarum infection
Lin, Z., Nie, H., Zhang, Y., Yin, Z., & Yan, X. (2022) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2022.101012 · Cited by 10
Genome-wide analysis of OFP gene family in pepper (Capsicum annuum L.)
Luo, Y., Yang, S., Luo, X., Li, J., Li, T., Tang, X., Liu, F., Zou, X., & Qin, C. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.941954 · Cited by 10
A likely autotetraploidization event shaped the Chinese mahogany (Toona sinensis) genome
Wang, J., Yang, Z., Lei, T., Zhang, Y., Xiao, Q., Yu, Z., Zhang, J., Sun, S., Xu, Q., Shen, S., et al. (2022) · Horticultural Plant Journal · doi:10.1016/j.hpj.2022.11.002 · Cited by 10
Natronogracilivirga saccharolytica gen. nov., sp. nov. and Cyclonatronum proteinivorum gen. nov., sp. nov., haloalkaliphilic organotrophic bacteroidetes from hypersaline soda lakes forming a new family Cyclonatronaceae fam. nov. in the order Balneolales
Zhilina, T. N., Sorokin, D. Y., Toshchakov, S. V., Kublanov, I. V., & Zavarzina, D. G. (2023) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2023.126403 · Cited by 10
New insights to diversity and enzyme–substrate interactions of fungal glucuronoyl esterases
Agger, J. W., Madsen, M. S., Martinsen, L. K., Martins, P. A., Barrett, K., & Meyer, A. S. (2023) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-023-12575-4 · Cited by 10
Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone
Voronezhskaya, V. S., Volkova, P., Bitarishvili, S. V., Shesterikova, E., Podlutskii, M., Clément, G., Meyer, C., Duarte, G. T., Kudin, M., Garbaruk, D., et al. (2023) · Plants · doi:10.3390/plants12122318 · Cited by 10
Identification of GA2ox Family Genes and Expression Analysis under Gibberellin Treatment in Pineapple (Ananas comosus (L.) Merr.)
Zhu, W., Qi, J., Chen, J., Ma, S., Liu, K., Su, H., Chai, M., Huang, Y., Xi, X., Cao, Z., et al. (2023) · Plants · doi:10.3390/plants12142673 · Cited by 10
MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets
Vik, D. R., Bolduc, B., Roux, S., Sun, C. L., Pratama, A. A., Krupovìč, M., & Sullivan, M. B. (2023) · ISME Communications · doi:10.1038/s43705-023-00295-9 · Cited by 10
A novel Vibrio alginolyticus phage and its therapy application in Portunus trituberculatus larvae
Cai, R., Li, D., Qin, W., Lin, W., Pan, L., Qian, M., Wang, F., Wang, C., Mu, C., & Tong, Y. (2023) · Aquaculture · doi:10.1016/j.aquaculture.2023.740165 · Cited by 10
Changes in m6A RNA methylation are associated with male sterility in wolfberry
Zhao, J., Zhang, C., Li, S., Yuan, M., Mu, W., Yang, J., Ma, Y., Guan, C., & Ma, C. (2023) · BMC Plant Biology · doi:10.1186/s12870-023-04458-7 · Cited by 10
Supramolecular Structures of the Dictyostelium Lamin NE81
Grafe, M., Batsios, P., Meyer, I., Lisin, D., Baumann, O., Goldberg, M. W., & Gräf, R. (2019) · Cells · doi:10.3390/cells8020162 · Cited by 10
Mining and Statistical Modeling of Natural and Variant Class IIa Bacteriocins Elucidate Activity and Selectivity Profiles across Species
Tresnak, D. T., & Hackel, B. J. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.01646-20 · Cited by 10
Complete genome analysis of an active prophage of Vibrio alginolyticus
Qin, W., Li, D., Xu, L., Lin, W., & Tong, Y. (2021) · Archives of Virology · doi:10.1007/s00705-020-04941-8 · Cited by 10
Draft Genome Sequences of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P, Isolated from Devil’s Hole, Bermuda
Buchholz, H. H., Michelsen, M. L., Parsons, R. J., Bates, N. R., & Temperton, B. (2021) · Microbiology Resource Announcements · doi:10.1128/mra.01325-20 · Cited by 10
Novel frameshift mutation in PURA gene causes severe encephalopathy of unclear cause
Spangenberg, L., Gueçaimburú, R., Tapié, A., Vivas, S., Rodríguez, S., Graña, M., Naya, H., & Raggio, V. E. (2021) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.1622 · Cited by 10
In silico identification of excretory/secretory proteins and drug targets in monogenean parasites
Caña‐Bozada, V. H., Chapa-López, M., Díaz-Martín, R. D., Garcı́a-Gasca, A., Huerta‐Ocampo, J. Á., de Anda‐Jáuregui, G., & Morales-Serna, F. N. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.104931 · Cited by 10
Structural basis of the membrane intramolecular transacylase reaction responsible for lyso-form lipoprotein synthesis
Olatunji, S., Bowen, K., Huang, C., Weichert, D., Singh, W., Tikhonova, I. G., Scanlan, E. M., Oliéric, V., & Caffrey, M. (2021) · Nature Communications · doi:10.1038/s41467-021-24475-0 · Cited by 10
How do I get the most out of my protein sequence using bioinformatics tools?
Pereira, J., & Alva, V. (2021) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798321007907 · Cited by 10
Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders
Woodard, J. C., Zheng, W. H., & Zhang, Y. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009370 · Cited by 10
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria
Dai, W., Li, J., Li, Q., Cai, J., Su, J., Stubenrauch, C. J., & Wang, J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab814 · Cited by 10
Lipid-Binding Aegerolysin from Biocontrol Fungus Beauveria bassiana
Kraševec, N., Panevska, A., Lemež, Š., Razinger, J., Sepčić, K., Anderluh, G., & Podobnik, M. (2021) · Toxins · doi:10.3390/toxins13110820 · Cited by 10
The choanoflagellate pore-forming lectin SaroL-1 punches holes in cancer cells by targeting the tumor-related glycosphingolipid Gb3
Notová, S., Bonnardel, F., Rosato, F., Šiukštaitė, L., Schwaiger, J., Lim, J. H., Bovin, N. V., Varrot, A., Ogawa, Y., Römer, W., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03869-w · Cited by 16
Identification of essential genes in Coxiella burnetii
Metters, G., Hemsley, C. M., Norville, I. H., & Titball, R. W. (2023) · Microbial Genomics · doi:10.1099/mgen.0.000944 · Cited by 11
Identification of MYB Transcription Factors Involving in Fruit Quality Regulation of Fragaria × ananassa Duch.
Wang, J., Yin, Y., Gao, H., & Sheng, L. (2022) · Genes · doi:10.3390/genes14010068 · Cited by 9
Genome-Wide Analysis of the Odorant Receptor Gene Family in Solenopsis invicta, Ooceraea biroi, and Monomorium pharaonis (Hymenoptera: Formicidae)
Zhang, B., Yang, R., Jiang, X., Xu, X., Wang, B., & Wang, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076624 · Cited by 9
Short-Term Supplementation of Pectin Alters Substrate Dynamics and Modulates Microbial Carbohydrate Metabolism in the Gut of a Pig Model
Xu, R., Feng, N., Li, Q., Wang, H., Su, Y., & Zhu, W. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c02562 · Cited by 9
Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii
Lin, H., Shi, T., Zhang, Y., He, C., Zhang, Q., Mo, Z., Pan, W., & Nie, X. (2023) · Plants · doi:10.3390/plants12142747 · Cited by 9
Genome-Wide Identification, Phylogeny and Expression Analysis of Subtilisin (SBT) Gene Family under Wheat Biotic and Abiotic Stress
Zhao, X., Goher, F., Chen, L., Song, J., & Zhao, J. (2023) · Plants · doi:10.3390/plants12173065 · Cited by 9
Expanded microbiome niches of RAG-deficient patients
Blaustein, R. A., Shen, Z., Kashaf, S. S., Lee-Lin, S.-Q., Conlan, S., Thomas, J., Mullikin, J. C., Young, A., Bouffard, G., Barnabas, B., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101205 · Cited by 9
Functional orthologs of honeybee CYP6AQ1 in stingless bees degrade the butenolide insecticide flupyradifurone
Xiao, X., Haas, J., & Nauen, R. (2023) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2023.115719 · Cited by 8
A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases
Narimatsu, Y., Büll, C., Taleb, V., Liao, Q., Compañón, I., Sánchez‐Navarro, D., Durbesson, F., Vincentelli, R., Hansen, L. H., Corzana, F., et al. (2024) · Nature Catalysis · doi:10.1038/s41929-024-01116-5 · Cited by 9
Genome-wide investigation of SQUAMOSA promoter binding protein-like genes in Liriodendron and functional characterization of LcSPL2
Zhang, Y., Hu, Q., Zhai, X., Tu, Z., Wang, J., Wang, M., & Li, H. (2024) · AoB Plants · doi:10.1093/aobpla/plae008 · Cited by 9
Genome-wide identification, expression analysis, and abiotic stress response of the CBL and CIPK gene families in Artocarpus nanchuanensis
Xia, C., Zhang, X., Zuo, Y., Zhang, X., Zhang, H., Wang, B., & Deng, H. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.131454 · Cited by 9
Molecular control of cellulosic fin morphogenesis in ascidians
Lanoizelet, M., Youhanna, C. E., Roure, A., & Darras, S. (2024) · BMC Biology · doi:10.1186/s12915-024-01872-7 · Cited by 9
Transition transferases prime bacterial capsule polymerization
Litschko, C., Domenico, V. D., Schulze, J., Li, S., Ovchinnikova, O. G., Voskuilen, T., Bethe, A., Cifuente, J. O., Marina, A., Budde, I., et al. (2024) · Nature Chemical Biology · doi:10.1038/s41589-024-01664-8 · Cited by 9
Genome-Wide Identification of GRAS Transcription Factors and Their Functional Analysis in Salt Stress Response in Sugar Beet
Hao, X., Gong, Y., Chen, S., Ma, C., & Duanmu, H. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25137132 · Cited by 10
“The domain composition and location information of the sugar beet GRAS transcription factors were obtained on the SMART website, and their conserved motifs were analyzed using the MEME online database (https://meme-suite.org/ accessed on 24 September 2022) [75] and visualized using TBtools [76].”
Method
CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes
Windels, A., Franceus, J., Pleiss, J., & Desmet, T. (2024) · PLoS ONE · doi:10.1371/journal.pone.0306410 · Cited by 9
Genome‐Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi‐Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves
Xu, C., Wang, J., Sun, L., Zhuang, L., Guo, Z., Ding, Q., Ma, D., Song, L., Li, J., Tang, H., et al. (2024) · Plant Cell & Environment · doi:10.1111/pce.15132 · Cited by 9
Genome-Wide Identification of the Remorin Gene Family in Poplar and Their Responses to Abiotic Stresses
Li, Z., Wang, H., Li, C., Liu, H., & Luo, J. (2024) · Life · doi:10.3390/life14101239 · Cited by 9
“After the findings from HMMER and BLASTP were combined, candidates for REM protein members were submitted to the HMMER database and the NCBI database (CDD) to verify conserved protein domains [47,48].”
Method
PatchProt: hydrophobic patch prediction using protein foundation models
Gogishvili, D., Minois-Genin, E., van Eck, J., & Abeln, S. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae154 · Cited by 11
“Generating a multiple sequence alignment is typically a rate-limiting step as it involves an exhaustive search of homologs (Camacho et al. 2009, Remmert et al. 2011, Potter et al. 2018, Mirdita et al. 2019).”
Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy
Khamespanah, E., Asad, S., Vanak, Z., & Mehrshad, M. (2024) · Microbial Ecology · doi:10.1007/s00248-024-02458-0 · Cited by 9
Genome-wide identification of the bHLH transcription factor family and the regulatory roles of PbbHLH74 in response to drought stress in Phoebe bournei
Fu, N., Wang, L., Sun, Q., Wang, Q., Zhang, Y., Han, X., Yang, Q., Ma, W., Tong, Z., & Zhang, J. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.137760 · Cited by 9
Development of a robust and efficient virus-induced gene silencing system for reverse genetics in recalcitrant Camellia drupifera capsules
Shen, H., Chen, H., Li, W., He, S., Liao, B., Xiong, W., Shen, Y., Li, Y., Gao, Y., Li, Y. Q., et al. (2025) · Plant Methods · doi:10.1186/s13007-024-01320-1 · Cited by 9
The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance
Yisilam, G., Zheng, E., Li, C., Zhang, Z., Su, Y., Chu, Z., Li, P., & Tian, X. (2025) · Acta Botanica Yunnanica · doi:10.1016/j.pld.2025.01.001 · Cited by 9
“HMMER v.3.1 (Potter et al., 2018) software with a hidden Markov model (HMM) pro ﬁ le was used to scan the NB-ARC (E-value 1e e 60) domain within the Pfam protein family (NB-ARC: PF00931).”
Influential
The Psu protein of phage satellite P4 inhibits transcription termination factor ρ by forced hyper-oligomerization
Gjorgjevikj, D., Kumar, N., Wang, B., Hilal, T., Said, N., Loll, B., Artsimovitch, I., Sen, R., & Wahl, M. C. (2025) · Nature Communications · doi:10.1038/s41467-025-55897-9 · Cited by 10
Effective Gene Expression Prediction and Optimization from Protein Sequences
Liu, T., Zhang, Y., Li, Y., Xu, G., Gao, H., Wang, P., Tu, T., Luo, H., Wu, N., Yao, B., et al. (2025) · Advanced Science · doi:10.1002/advs.202407664 · Cited by 9
Genome-wide identification and comparative analysis of the AP2/ERF gene family in Prunus dulcis and Prunus tenella: expression of PdAP2/ERF genes under freezing stress during dormancy
Zhang, D., Zeng, B., He, Y., Li, J., & Yu, Z. (2025) · BMC Genomics · doi:10.1186/s12864-025-11275-9 · Cited by 9
“The protein data of both genomes were compared against the AP2 domain Hidden Markov Model (PF00847), retaining genes with an e-value less than or equal to e − 5 [35].”
Genome-wide identification of five fern bHLH families and functional analysis of bHLHs in lignin biosynthesis in Alsophila spinulosa
Huang, X., Fan, J., Liu, C., Wang, P., Li, H., Wang, G., & Chen, X. (2025) · BMC Genomics · doi:10.1186/s12864-025-11522-z · Cited by 9
OriV-Finder: a comprehensive web server for bacterial plasmid replication origin analysis
Li, Y., & Gao, F. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf341 · Cited by 9
NIN-like proteins in poplar play roles in responding to abiotic stresses and nitrate availability
Guan, L., Lu, Y., Wang, H., Li, Z., Li, Q., & Luo, J. (2025) · Plant Stress · doi:10.1016/j.stress.2025.100878 · Cited by 10
Comprehensive genome-wide analysis and functional characterization of the DIR gene family in Herpetospermum pedunculosum: insights from HpDIR16 and HpDIR17
Chen, D., Sun, M., Yang, Y., Tan, B., Ren, D., Yang, T., Li, R., & Zhao, Q. (2025) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2025.110074 · Cited by 9
Evolution of terpene synthases in the sesquiterpene biosynthesis pathway and analysis of their transcriptional regulatory network in Asteraceae
Yang, X., Meng, F., Cheng, Q., Feng, P., Song, X., & Chen, W. (2025) · Horticulture Research · doi:10.1093/hr/uhaf229 · Cited by 9
“Protein sequences from 25 species were retrieved using HMMER tool (v 2.3.2) with default parameters [57].”
Influential
Deciphering functional landscapes of rumen microbiota unveils the role of Prevotella bryantii in milk fat synthesis in goats
Yu, L., Zheng, Y., Yan, Y., Zhang, K., Sun, X., Yang, B., Ge, L., Meng, Z., Cao, X., Zhang, X., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03788-z · Cited by 10
“CAZyme annotations were performed using HMMER [76] (v3.”
Directed evolution of phages in biofilms enhances Pseudomonas aeruginosa control through improved lipopolysaccharide recognition
Meneses, L., Valentová, L., Santos, S. R. B., Erdmann, J., Crabbé, A., Plevka, P., Häußler, S., Pires, D. P., Coenye, T., & Azeredo, J. (2025) · Nature Communications · doi:10.1038/s41467-025-65014-5 · Cited by 11
“For functional annotation, protein homology results were complemented using BLASTP 21 and HMMER 56 , conserved domains and families were identi ﬁ ed using InterPro 57 and CDD 58 , transmembrane domains and signal peptide cleavage sites were identi ﬁ ed by TMHMM 59 , Phobius 60 , SignalIP 61 and…”
Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review
Galeeva, J. S., Kuzmichenko, P., Manolov, A. I., Lukashev, A. N., & Ilina, E. N. (2025) · Viruses · doi:10.3390/v17121538 · Cited by 9
“HMMER is a widely adopted software implementation of profile HMMs for biological sequence analysis [53].”
Nutrient balance regulates soil microbial health under long-term fertilization
Lin, D., Ma, Q., Ye, Y.-Q., Wanek, W., Gregory, A. S., Jones, D. M., Graham, D. W., Zhu, D., Peñuelas, J., & Zhu, Y.-G. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117274 · Cited by 9
Cloning and functional complementation of ten Schistosoma mansoni phosphodiesterases expressed in the mammalian host stages
Munday, J. C., Kunz, S., Kalejaiye, T. D., Siderius, M. H., Schroeder, S., Paape, D., Al-Ghamdi, A., Abbasi, Z., Huang, S. X., Donachie, A., et al. (2020) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0008447 · Cited by 9
Genome-Wide Identification, Comparison, and Expression Analysis of Transcription Factors in Ascidian Styela clava
Zhang, J., Wei, J., Yu, H., & Dong, B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094317 · Cited by 9
Reannotation of Mycoplasma hyopneumoniae hypothetical proteins revealed novel potential virulence factors
Tavares, B. A. D. R., Paes, J. A., Zaha, A., & Ferreira, H. B. (2021) · Microbial Pathogenesis · doi:10.1016/j.micpath.2021.105344 · Cited by 9
The grapevine aspartic protease gene family: characterization and expression modulation in response to Plasmopara viticola
Figueiredo, L., Santos, R. B., & Figueiredo, A. (2022) · Journal of Plant Research · doi:10.1007/s10265-022-01390-z · Cited by 9
Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane
de Oliveira, L. P., Navarro, B. V., Pereira, J. P. D. J., Lopes, A. R., Martins, M. C. M., Riaño‐Pachón, D. M., & Buckeridge, M. S. (2022) · Scientific Reports · doi:10.1038/s41598-022-11508-x · Cited by 11
Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L.
Li, Y., Wang, Y., Feng, X., Hua, X., Dou, M., Yao, W., Zhang, M., & Zhang, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23158724 · Cited by 9
RNAi-Mediated Manipulation of Cuticle Coloration Genes in Lygus hesperus Knight (Hemiptera: Miridae)
Brent, C. S., Heu, C. C., Gross, R. J., Fan, B., Langhorst, D., & Hull, J. J. (2022) · Insects · doi:10.3390/insects13110986 · Cited by 9
Comparative Genomic Analysis of the Thiolase Family and Functional Characterization of the Acetyl-Coenzyme A Acyltransferase-1 Gene for Milk Biosynthesis and Production of Buffalo and Cattle
Deng, T., Wu, J., Abdel-Shafy, H., Wang, X., Lv, H., Shaukat, A., Zhou, X., Zhou, Y., Sun, H., Wei, P., et al. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.2c07763 · Cited by 9
Two Complete Genomes of Male-Killing Wolbachia Infecting Ostrinia Moth Species Illuminate Their Evolutionary Dynamics and Association with Hosts
Muro, T., Hikida, H., Fujii, T., Kiuchi, T., & Katsuma, S. (2023) · Microbial Ecology · doi:10.1007/s00248-023-02198-7 · Cited by 11
Phylogenomics reveals insights into the functional evolution of the genus Agrobacterium and enables the description of Agrobacterium divergens sp. nov
Naranjo, H. D., Lebbe, L., Cnockaert, M. C., Lassalle, F., Too, C. C., & Willems, A. (2023) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2023.126420 · Cited by 9
Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein N -acyltransferase
Smithers, L., Degtjarik, O., Weichert, D., Huang, C., Boland, C., Bowen, K., Oluwole, A. O., Lutomski, C. A., Robinson, C. V., Scanlan, E. M., et al. (2023) · Science Advances · doi:10.1126/sciadv.adf5799 · Cited by 8
Genome-centric investigation of the potential succession pattern in gut microbiota and altered functions under high-protein diet
Zhao, Y., Chen, L., Yao, S., Chen, L., Huang, J., Chen, S., & Yu, Z. (2023) · Current Research in Food Science · doi:10.1016/j.crfs.2023.100600 · Cited by 11
Barley Nodulin 26-like intrinsic protein permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification
Venkataraghavan, A., Kim, H. S., Schwerdt, J. G., Gulyuk, A. V., Singh, A., Yingling, Y. G., Tyerman, S. D., & Hrmová, M. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105410 · Cited by 9
A defining member of the new cysteine-cradle family is an aECM protein signalling skin damage in C. elegans
Sonntag, T., Omi, S., Andreeva, A., Valotteau, C., Eichelbrenner, J., Chisholm, A. D., Ward, J. D., & Pujol, N. (2025) · PLOS Genetics · doi:10.1371/journal.pgen.1011593 · Cited by 9
“We iteratively searched for homologues using the HMMER package [66] and used an inclusion threshold of 27 bits.”

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

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.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

HMMER web server: 2018 update

Abstract

Overview

Integrity signals

Figures

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks