{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T22:34:46Z","timestamp":1717713286395},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,8,12]]},"abstract":"Abstract<\/jats:title>\n Motivation: Phylogenetic shadowing is a comparative genomics principle that allows for the discovery of conserved regions in sequences from multiple closely related organisms. We develop a formal probabilistic framework for combining phylogenetic shadowing with feature-based functional annotation methods. The resulting model, a generalized hidden Markov phylogeny (GHMP), applies to a variety of situations where functional regions are to be inferred from evolutionary constraints.<\/jats:p>\n Results: We show how GHMPs can be used to predict complete shared gene structures in multiple primate sequences. We also describe shadower, our implementation of such a prediction system. We find that shadower outperforms previously reported ab initio gene finders, including comparative human\u2013mouse approaches, on a small sample of diverse exonic regions. Finally, we report on an empirical analysis of shadower's performance which reveals that as few as five well-chosen species may suffice to attain maximal sensitivity and specificity in exon demarcation.<\/jats:p>\n Availability: A Web server is available at http:\/\/bonaire.lbl.gov\/shadower<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth153","type":"journal-article","created":{"date-parts":[[2004,3,2]],"date-time":"2004-03-02T21:41:06Z","timestamp":1078263666000},"page":"1850-1860","source":"Crossref","is-referenced-by-count":31,"title":["Multiple-sequence functional annotation and the generalized hidden Markov phylogeny"],"prefix":"10.1093","volume":"20","author":[{"given":"Jon D.","family":"McAuliffe","sequence":"first","affiliation":[]},{"given":"Lior","family":"Pachter","sequence":"additional","affiliation":[]},{"given":"Michael I.","family":"Jordan","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,2,26]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/12\/1850\/48905858\/bioinformatics_20_12_1850.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/12\/1850\/48905858\/bioinformatics_20_12_1850.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:34:02Z","timestamp":1674664442000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/12\/1850\/218005"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,2,26]]},"references-count":0,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2004,8,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth153","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,8,12]]},"published":{"date-parts":[[2004,2,26]]}}}