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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- 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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