KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold
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Summary: KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction. Availability: KofamKOALA, KofamScan, and KOfam are freely available from https://www.genome.jp/tools/kofamkoala/ Contact: ogata@kuicr.kyoto-u.ac.jp
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Additional functional analyses are provided in the form of KEGG orthologue annotations, calculated using HMMER and the KOfam library on predicted protein sequences.
“Additional functional analyses are also provided in the form of KEGG orthologue (KO) (23) annotations, which are calculated using HMMER (40) and the KOfam library (using a slightly modified form of the profile hidden Markov model (HMM) database of KEGG orthologues (41)) on the predicted protein sequences.”
From MGnify: the microbiome analysis resource in 2020 (2019) · cites this paper as [41]
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works
Self-citationKEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works
Self-citationCd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175 · see citing works
MAFFT version 5: improvement in accuracy of multiple sequence alignment
Katoh, K., Kuma, K., Toh, H., & Miyata, T. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki198 · Cited by 5,063 · see citing works
KAAS: an automatic genome annotation and pathway reconstruction server
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C., & Kanehisa, M. I. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm321 · Cited by 4,128 · see citing works
Self-citationKanehisa, M., Sato, Y., & Morishima, K. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.11.006 · Cited by 3,810 · see citing works
Self-citationEddy, S. R. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000069 · Cited by 351 · see citing works
Suzuki, S., Kakuta, M., Ishida, T., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0103833 · Cited by 87 · see citing works
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Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1035 · Cited by 562 · see citing works
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Zepeda-Rivera, M., Minot, S. S., Bouzek, H., Wu, H., Blanco-Míguez, A., Manghi, P., Jones, D. S., LaCourse, K. D., Wu, Y., McMahon, E. F., et al. (2024) · Nature · doi:10.1038/s41586-024-07182-w · Cited by 451 · see citing works
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Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J., & Williams, T. A. (2021) · Science · doi:10.1126/science.abe0511 · Cited by 285 · see citing works
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Karcher, N., Nigro, E., Punčochář, M., Blanco-Míguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02427-7 · Cited by 159 · see citing works
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Ghaly, T. M., Rajabal, V., Russell, D., Colombi, E., & Tetu, S. G. (2025) · doi:10.1101/2025.04.02.646905 · Cited by 5 · see citing works
- Authors
- Aramaki, T., Blanc-Mathieu, R., Endo, H., Ohkubo, K., Kanehisa, M., Goto, S., & Ogata, H.
- Affiliations
- Kyoto University (JP)
- Research Organization of Information and Systems (JP)
- Corresponding author
- Ogata, Hiroyuki
- Venue
- Bioinformatics
- Publisher
- openRxiv
- Published
- 2019-04-08
- Volume
- 36
- Issue
- 7
- Pages
- 2251-2252
- ISSN
- 1367-4803 (ISSN-L)
- PMC
- PMC7141845
- OpenAlex
- W2991239467
- Cited by
- 2,054
- References
- 9
- Citations by year
- 2026: 392 · 2025: 421 · 2024: 417 · 2023: 321 · 2022: 242 · 2021: 174 · 2020: 73 · 2019: 12
- FWCI
- 42.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Institutional Repositories DataBase (IRDB) (submittedVersion, other-oa)
- Kyoto University Research Information Repository (Kyoto University) (submittedVersion, cc-by-nc)
- Funders
- Ministry of Education, Culture, Sports, Science and Technology (16K21723, 16H06429, 16K21723, 18H02279, 16H06437, 26430184, 16H06429)
- Japan Society for the Promotion of Science (26430184, 16K21723, 16H06429, 18H02279, 16H06437)
- Institute for Chemical Research, Kyoto University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- profile hidden Markov models, protein annotation, homology search, KEGG pathways, web server
- MeSH terms
- Amino Acid Sequence, Computers, Databases, Factual
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