{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T21:29:17Z","timestamp":1767907757287,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Orphan genes, also known as ORFans, are newly evolved genes in a genome that enable the organism to adapt to specific living environment. The gene content of every sequenced genome can be classified into different age groups, based on how widely\/narrowly a gene\u2019s homologs are distributed in the context of species taxonomy. Those having homologs restricted to organisms of particular taxonomic ranks are classified as taxonomically restricted ORFans.<\/jats:p>\n               <jats:p>Results: Implementing this idea, we have developed an open source program named ORFanFinder and a free web server to allow automated classification of a genome\u2019s gene content and identification of ORFans at different taxonomic ranks. ORFanFinder and its web server will contribute to the comparative genomics field by facilitating the study of the origin of new genes and the emergence of lineage-specific traits in both prokaryotes and eukaryotes.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/cys.bios.niu.edu\/orfanfinder<\/jats:p>\n               <jats:p>Contact: \u00a0yyin@niu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw122","type":"journal-article","created":{"date-parts":[[2016,3,9]],"date-time":"2016-03-09T01:38:23Z","timestamp":1457487503000},"page":"2053-2055","source":"Crossref","is-referenced-by-count":17,"title":["ORFanFinder: automated identification of taxonomically restricted orphan genes"],"prefix":"10.1093","volume":"32","author":[{"given":"Alex","family":"Ekstrom","sequence":"first","affiliation":[{"name":"1 Department of Computer Science"}]},{"given":"Yanbin","family":"Yin","sequence":"additional","affiliation":[{"name":"2 Department of Biological Sciences, Montgomery Hall 325A, Northern Illinois University, DeKalb, IL, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,3,7]]},"reference":[{"key":"2023020112334370400_btw122-B1","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/nature11184","article-title":"Proto-genes and de novo gene birth","volume":"487","author":"Carvunis","year":"2012","journal-title":"Nature"},{"key":"2023020112334370400_btw122-B2","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1038\/nrg3521","article-title":"New genes as drivers of phenotypic evolution","volume":"14","author":"Chen","year":"2013","journal-title":"Nat. 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