{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T17:06:45Z","timestamp":1770916005659,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2022,3,31]],"date-time":"2022-03-31T00:00:00Z","timestamp":1648684800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2015-05342"],"award-info":[{"award-number":["2015-05342"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009244","name":"Stockholm University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009244","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Predicting orthologs, genes in different species having shared ancestry, is an important task in bioinformatics. Orthology prediction tools are required to make accurate and fast predictions, in order to analyze large amounts of data within a feasible time frame. InParanoid is a well-known algorithm for orthology analysis, shown to perform well in benchmarks, but having the major limitation of long runtimes on large datasets. Here, we present an update to the InParanoid algorithm that can use the faster tool DIAMOND instead of BLAST for the homolog search step. We show that it reduces the runtime by 94%, while still obtaining similar performance in the Quest for Orthologs benchmark.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code is available at (https:\/\/bitbucket.org\/sonnhammergroup\/inparanoid).<\/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\/btac194","type":"journal-article","created":{"date-parts":[[2022,3,29]],"date-time":"2022-03-29T11:38:06Z","timestamp":1648553886000},"page":"2918-2919","source":"Crossref","is-referenced-by-count":34,"title":["InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0532-8251","authenticated-orcid":false,"given":"Emma","family":"Persson","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , 17121 Solna, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9015-5588","authenticated-orcid":false,"given":"Erik L L","family":"Sonnhammer","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , 17121 Solna, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2022,3,31]]},"reference":[{"key":"2023020109082269200_btac194-B1","doi-asserted-by":"crossref","first-page":"e1002514","DOI":"10.1371\/journal.pcbi.1002514","article-title":"Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs","volume":"8","author":"Altenhoff","year":"2012","journal-title":"PLoS Comput. Biol"},{"key":"2023020109082269200_btac194-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. Methods"},{"key":"2023020109082269200_btac194-B3","doi-asserted-by":"crossref","first-page":"W538","DOI":"10.1093\/nar\/gkaa308","article-title":"The Quest for Orthologs benchmark service and consensus calls in 2020","volume":"48","author":"Altenhoff","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023020109082269200_btac194-B4","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. 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Zool"},{"key":"2023020109082269200_btac194-B9","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1186\/1471-2105-12-124","article-title":"Proteinortho: detection of (co-)orthologs in large-scale analysis","volume":"12","author":"Lechner","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020109082269200_btac194-B10","first-page":"20","article-title":"Ten years of collaborative progress in the Quest for Orthologs","volume":"8","author":"Linard","year":"2021","journal-title":"Mol. Biol. 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