{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:14:24Z","timestamp":1784074464236,"version":"3.55.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T00:00:00Z","timestamp":1531958400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Japanese Society for the Promotion of Scienc","award":["16H06154"],"award-info":[{"award-number":["16H06154"]}]},{"name":"Japanese Society for the Promotion of Scienc","award":["16H06279"],"award-info":[{"award-number":["16H06279"]}]},{"name":"Japanese Society for the Promotion of Scienc","award":["17H05834"],"award-info":[{"award-number":["17H05834"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Orthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target genes for biotechnological applications and revealing the evolutionary history of life. Although its importance keeps rising with the ever-growing number of sequenced genomes, existing tools are computationally demanding and difficult to employ.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we present SonicParanoid, which is faster than, but comparably accurate to, the well-established tools with a balanced precision-recall trade-off. Furthermore, SonicParanoid substantially relieves the difficulties of orthology inference for those who need to construct and maintain their own genomic datasets.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>SonicParanoid is available with a GNU GPLv3 license on the Python Package Index and BitBucket. Documentation is available at http:\/\/iwasakilab.bs.s.u-tokyo.ac.jp\/sonicparanoid.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty631","type":"journal-article","created":{"date-parts":[[2018,7,14]],"date-time":"2018-07-14T17:43:43Z","timestamp":1531590223000},"page":"149-151","source":"Crossref","is-referenced-by-count":144,"title":["SonicParanoid: fast, accurate and easy orthology inference"],"prefix":"10.1093","volume":"35","author":[{"given":"Salvatore","family":"Cosentino","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1066-8659","authenticated-orcid":false,"given":"Wataru","family":"Iwasaki","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan"},{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan"},{"name":"Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,7,19]]},"reference":[{"key":"2023013107204529100_bty631-B1","doi-asserted-by":"crossref","first-page":"e9","DOI":"10.1093\/bioinformatics\/btl213","article-title":"Automatic clustering of orthologs and inparalogs shared by multiple proteomes","volume":"22","author":"Alexeyenko","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013107204529100_bty631-B2","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/nmeth.3830","article-title":"Standardized benchmarking in the quest for orthologs","volume":"13","author":"Altenhoff","year":"2016","journal-title":"Nat. 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