{"title":"一个精确的算法,以识别基序在同源序列从多个物种。","authors":"M Blanchette, B Schwikowski, M Tompa","doi":"","DOIUrl":null,"url":null,"abstract":"<p><p>The identification of sequence motifs is a fundamental method for suggesting good candidates for biologically functional regions such as promoters, splice sites, binding sites, etc. We investigate the following approach to identifying motifs: given a collection of orthologous sequences from multiple species related by a known phylogenetic tree, search for motifs that are well conserved (according to a parsimony measure) in the species. We present an exact algorithm for solving this problem. We then discuss experimental results on finding promoters of the rbcS gene for a family of 10 plants, on finding promoters of the adh gene for 12 Drosophila species, and on finding promoters of several chloroplast encoded genes.</p>","PeriodicalId":79420,"journal":{"name":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2000-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"An exact algorithm to identify motifs in orthologous sequences from multiple species.\",\"authors\":\"M Blanchette, B Schwikowski, M Tompa\",\"doi\":\"\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The identification of sequence motifs is a fundamental method for suggesting good candidates for biologically functional regions such as promoters, splice sites, binding sites, etc. We investigate the following approach to identifying motifs: given a collection of orthologous sequences from multiple species related by a known phylogenetic tree, search for motifs that are well conserved (according to a parsimony measure) in the species. We present an exact algorithm for solving this problem. We then discuss experimental results on finding promoters of the rbcS gene for a family of 10 plants, on finding promoters of the adh gene for 12 Drosophila species, and on finding promoters of several chloroplast encoded genes.</p>\",\"PeriodicalId\":79420,\"journal\":{\"name\":\"Proceedings. International Conference on Intelligent Systems for Molecular Biology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2000-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Proceedings. International Conference on Intelligent Systems for Molecular Biology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proceedings. International Conference on Intelligent Systems for Molecular Biology","FirstCategoryId":"1085","ListUrlMain":"","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
An exact algorithm to identify motifs in orthologous sequences from multiple species.
The identification of sequence motifs is a fundamental method for suggesting good candidates for biologically functional regions such as promoters, splice sites, binding sites, etc. We investigate the following approach to identifying motifs: given a collection of orthologous sequences from multiple species related by a known phylogenetic tree, search for motifs that are well conserved (according to a parsimony measure) in the species. We present an exact algorithm for solving this problem. We then discuss experimental results on finding promoters of the rbcS gene for a family of 10 plants, on finding promoters of the adh gene for 12 Drosophila species, and on finding promoters of several chloroplast encoded genes.