{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T15:17:27Z","timestamp":1778944647048,"version":"3.51.4"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2018,8,1]],"date-time":"2018-08-01T00:00:00Z","timestamp":1533081600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fulton Supercomputing Laboratory at Brigham Young University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Orthologous gene identification is fundamental to all aspects of biology. For example, ortholog identification between species can provide functional insights for genes of unknown function and is a necessary step in phylogenetic inference. Currently, most ortholog identification algorithms require all-versus-all BLAST comparisons, which are time-consuming and memory intensive.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In contrast to existing approaches, JustOrthologs exploits the conservation of gene structure by using the lengths of coding sequence regions and dinucleotide percentages to identify orthologs. In comparison to OrthoMCL, OMA and OrthoFinder, JustOrthologs decreases ortholog identification runtime by more than 96% and achieves comparable precision and recall scores. The computational speedup allowed us to conduct pairwise comparisons of 1197 complete genomes (780 eukaryotes and 417 archaea). We confirmed gene annotations for 384\u2009120 genes, grouped 1\u2009675\u2009415 genes in previously unreported ortholog groups, and identified 51\u2009429 potentially mislabeled genes across 622\u2009843 ortholog groups.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>JustOrthologs is an open source collaborative software package available in the GitHub repository: https:\/\/github.com\/ridgelab\/JustOrthologs\/. All test FASTA files used for comparisons are freely available at https:\/\/github.com\/ridgelab\/JustOrthologs\/comparisonFastaFiles\/. Reference genomes used in this work are available for download from the NCBI repository: ftp:\/\/ftp.ncbi.nih.gov\/genomes\/.<\/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\/bty669","type":"journal-article","created":{"date-parts":[[2018,7,31]],"date-time":"2018-07-31T21:54:03Z","timestamp":1533074043000},"page":"546-552","source":"Crossref","is-referenced-by-count":23,"title":["JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm"],"prefix":"10.1093","volume":"35","author":[{"given":"Justin B","family":"Miller","sequence":"first","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brandon D","family":"Pickett","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Perry G","family":"Ridge","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,8,1]]},"reference":[{"key":"2023051510510002400_bty669-B1","doi-asserted-by":"crossref","first-page":"D240","DOI":"10.1093\/nar\/gku1158","article-title":"The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements","volume":"43","author":"Altenhoff","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023051510510002400_bty669-B2","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. 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