{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T05:59:40Z","timestamp":1700546380653},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference.<\/jats:p>\n               <jats:p>Results: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (\u223c1400 bp), restricted to hominoids, can be predicted to be functional in \u223c94\u2013100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale.<\/jats:p>\n               <jats:p>Availability: ReEVOLVER is available at .<\/jats:p>\n               <jats:p>Contact: \u00a0Henrik.Kaessmann@unil.ch<\/jats:p>\n               <jats:p>Supplementary Data: Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl280","type":"journal-article","created":{"date-parts":[[2006,6,10]],"date-time":"2006-06-10T00:49:11Z","timestamp":1149900551000},"page":"1815-1822","source":"Crossref","is-referenced-by-count":9,"title":["Evolutionary simulations to detect functional lineage-specific genes"],"prefix":"10.1093","volume":"22","author":[{"given":"Isabelle","family":"Dupanloup","sequence":"first","affiliation":[{"name":"Center for Integrative Genomics, University of Lausanne 1 \u00a0 1 \u00a0 \u00a0 CH-1015 Lausanne, Switzerland"},{"name":"Computational and Molecular Population Genetics Lab, Zoological Institute, University of Bern 2 \u00a0 2 \u00a0 \u00a0 CH-3012 Bern, Switzerland"}]},{"given":"Henrik","family":"Kaessmann","sequence":"additional","affiliation":[{"name":"Center for Integrative Genomics, University of Lausanne 1 \u00a0 1 \u00a0 \u00a0 CH-1015 Lausanne, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2006,6,9]]},"reference":[{"key":"2023012409105041400_b1","doi-asserted-by":"crossref","first-page":"1854","DOI":"10.1101\/gr.604902","article-title":"Retroposed new genes out of the X in Drosophila","volume":"12","author":"Betran","year":"2002","journal-title":"Genome Res."},{"key":"2023012409105041400_b2","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1126\/science.1081331","article-title":"Phylogenetic shadowing of primate sequences to find functional regions of the human genome","volume":"299","author":"Boffelli","year":"2003","journal-title":"Science"},{"key":"2023012409105041400_b3","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1038\/nrg1350","article-title":"Comparative genomics at the vertebrate extremes","volume":"5","author":"Boffelli","year":"2004","journal-title":"Nat. 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