{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,18]],"date-time":"2023-08-18T01:24:36Z","timestamp":1692321876841},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3240,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Practitioners of comparative genomics face huge analytical challenges as whole genome sequences and functional\/expression data accumulate. Furthermore, the field would greatly benefit from a better integration of this wealth of data with evolutionary concepts.<\/jats:p>\n               <jats:p>Results: Here, we present MANTIS, a relational database for the analysis of (i) gains and losses of genes on specific branches of the metazoan phylogeny, (ii) reconstructed genome content of ancestral species and (iii) over- or under-representation of functions\/processes and tissue specificity of gained, duplicated and lost genes. MANTIS estimates the most likely positions of gene losses on the true phylogeny using a maximum-likelihood function. A user-friendly interface and an extensive query system allow to investigate questions pertaining to gene identity, phylogenetic mapping and function\/expression parameters.<\/jats:p>\n               <jats:p>Availability: MANTIS is freely available at http:\/\/www.mantisdb.org and constitutes the missing link between multi-species genome comparisons and functional analyses.<\/jats:p>\n               <jats:p>Contact: mcmilink@ulb.ac.be<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm567","type":"journal-article","created":{"date-parts":[[2007,11,20]],"date-time":"2007-11-20T01:13:06Z","timestamp":1195521186000},"page":"151-157","source":"Crossref","is-referenced-by-count":6,"title":["MANTIS: a phylogenetic framework for multi-species genome comparisons"],"prefix":"10.1093","volume":"24","author":[{"given":"Athanasia C.","family":"Tzika","sequence":"first","affiliation":[{"name":"1 Laboratory of Evolutionary Genetics, Institute for Molecular Biology & Medicine, Universit\u00e9 Libre de Bruxelles, 12 rue Jeener & Brachet, B6041 Gosselies and 2Bioinformatics & Evolutionary Genomics, Department of Plant Systems Biology, Ghent University, VIB, Gent, Belgium"}]},{"given":"Rapha\u00ebl","family":"Helaers","sequence":"additional","affiliation":[{"name":"1 Laboratory of Evolutionary Genetics, Institute for Molecular Biology & Medicine, Universit\u00e9 Libre de Bruxelles, 12 rue Jeener & Brachet, B6041 Gosselies and 2Bioinformatics & Evolutionary Genomics, Department of Plant Systems Biology, Ghent University, VIB, Gent, Belgium"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"1 Laboratory of Evolutionary Genetics, Institute for Molecular Biology & Medicine, Universit\u00e9 Libre de Bruxelles, 12 rue Jeener & Brachet, B6041 Gosselies and 2Bioinformatics & Evolutionary Genomics, Department of Plant Systems Biology, Ghent University, VIB, Gent, Belgium"}]},{"given":"Michel C.","family":"Milinkovitch","sequence":"additional","affiliation":[{"name":"1 Laboratory of Evolutionary Genetics, Institute for Molecular Biology & Medicine, Universit\u00e9 Libre de Bruxelles, 12 rue Jeener & Brachet, B6041 Gosselies and 2Bioinformatics & Evolutionary Genomics, Department of Plant Systems Biology, Ghent University, VIB, Gent, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2007,11,19]]},"reference":[{"key":"2023020209475359800_B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. 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