{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T12:56:34Z","timestamp":1776430594230,"version":"3.51.2"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,11,19]],"date-time":"2019-11-19T00:00:00Z","timestamp":1574121600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"JSPS\/MEXT\/KAKENHI","award":["26430184"],"award-info":[{"award-number":["26430184"]}]},{"name":"JSPS\/MEXT\/KAKENHI","award":["18H02279"],"award-info":[{"award-number":["18H02279"]}]},{"name":"JSPS\/MEXT\/KAKENHI","award":["16H06429"],"award-info":[{"award-number":["16H06429"]}]},{"name":"JSPS\/MEXT\/KAKENHI","award":["16K21723"],"award-info":[{"award-number":["16K21723"]}]},{"name":"JSPS\/MEXT\/KAKENHI","award":["16H06437"],"award-info":[{"award-number":["16H06437"]}]},{"name":"Collaborative Research Program of the Institute for Chemical Research, Kyoto University","award":["2018-30"],"award-info":[{"award-number":["2018-30"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https:\/\/www.genome.jp\/tools\/kofamkoala\/).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz859","type":"journal-article","created":{"date-parts":[[2019,11,18]],"date-time":"2019-11-18T06:36:19Z","timestamp":1574058979000},"page":"2251-2252","source":"Crossref","is-referenced-by-count":1605,"title":["KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold"],"prefix":"10.1093","volume":"36","author":[{"given":"Takuya","family":"Aramaki","sequence":"first","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University , Gokasho, Uji, Kyoto 611-0011"}]},{"given":"Romain","family":"Blanc-Mathieu","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University , Gokasho, Uji, Kyoto 611-0011"}]},{"given":"Hisashi","family":"Endo","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University , Gokasho, Uji, Kyoto 611-0011"}]},{"given":"Koichi","family":"Ohkubo","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University , Gokasho, Uji, Kyoto 611-0011"},{"name":"Hewlett-Packard Japan Ltd. , Koto-ku, Tokyo 136-8711"}]},{"given":"Minoru","family":"Kanehisa","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University , Gokasho, Uji, Kyoto 611-0011"}]},{"given":"Susumu","family":"Goto","sequence":"additional","affiliation":[{"name":"Database Center for Life Science, Research Organization of Information and Systems , Kashiwa, Chiba 277-0871, Japan"}]},{"given":"Hiroyuki","family":"Ogata","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University , Gokasho, Uji, Kyoto 611-0011"}]}],"member":"286","published-online":{"date-parts":[[2019,11,19]]},"reference":[{"key":"2023062300073444800_btz859-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023062300073444800_btz859-B2","doi-asserted-by":"crossref","first-page":"e1000069","DOI":"10.1371\/journal.pcbi.1000069","article-title":"A probabilistic model of local sequence alignment that simplifies statistical significance estimation","volume":"4","author":"Eddy","year":"2008","journal-title":"PLoS Comput. 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