Lingxi Zhou, William Hoskins, Jieyi Zhao, Jijun Tang
{"title":"加权最大匹配下的祖先重构","authors":"Lingxi Zhou, William Hoskins, Jieyi Zhao, Jijun Tang","doi":"10.1109/BIBM.2015.7359889","DOIUrl":null,"url":null,"abstract":"Ancestral genome reconstruction has attracted increasing interests from both biologists and computer scientists. It has been conducted using various evolutionary models ever since comparative genomics moved from sequence data to gene order data. We propose a Flexible Ancestral Reconstruction Model, FARM, based on the maximum likelihood and weighted maximum matching algorithms, to infer ancestral gene orders. This will accommodate various evolutionary scenarios, including not only genomic rearrangements, but also insertion/deletions (indels), segment duplications, and whole genome duplications. We evaluate this work by using various simulated evolution experiments while comparing FARM to existing methods, like InferCarsPro, GASTS and PMAG++. FARM shows significant improvement in running time and the final assembling process and, therefore, can be used in large-scale real biological data ancestral inference.","PeriodicalId":186217,"journal":{"name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"14 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2015-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"6","resultStr":"{\"title\":\"Ancestral reconstruction under weighted maximum matching\",\"authors\":\"Lingxi Zhou, William Hoskins, Jieyi Zhao, Jijun Tang\",\"doi\":\"10.1109/BIBM.2015.7359889\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Ancestral genome reconstruction has attracted increasing interests from both biologists and computer scientists. It has been conducted using various evolutionary models ever since comparative genomics moved from sequence data to gene order data. We propose a Flexible Ancestral Reconstruction Model, FARM, based on the maximum likelihood and weighted maximum matching algorithms, to infer ancestral gene orders. This will accommodate various evolutionary scenarios, including not only genomic rearrangements, but also insertion/deletions (indels), segment duplications, and whole genome duplications. We evaluate this work by using various simulated evolution experiments while comparing FARM to existing methods, like InferCarsPro, GASTS and PMAG++. FARM shows significant improvement in running time and the final assembling process and, therefore, can be used in large-scale real biological data ancestral inference.\",\"PeriodicalId\":186217,\"journal\":{\"name\":\"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)\",\"volume\":\"14 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2015-11-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"6\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/BIBM.2015.7359889\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/BIBM.2015.7359889","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Ancestral reconstruction under weighted maximum matching
Ancestral genome reconstruction has attracted increasing interests from both biologists and computer scientists. It has been conducted using various evolutionary models ever since comparative genomics moved from sequence data to gene order data. We propose a Flexible Ancestral Reconstruction Model, FARM, based on the maximum likelihood and weighted maximum matching algorithms, to infer ancestral gene orders. This will accommodate various evolutionary scenarios, including not only genomic rearrangements, but also insertion/deletions (indels), segment duplications, and whole genome duplications. We evaluate this work by using various simulated evolution experiments while comparing FARM to existing methods, like InferCarsPro, GASTS and PMAG++. FARM shows significant improvement in running time and the final assembling process and, therefore, can be used in large-scale real biological data ancestral inference.