加权最大匹配下的祖先重构

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}
引用次数: 6

摘要

祖先基因组重建已经引起了生物学家和计算机科学家越来越多的兴趣。自从比较基因组学从序列数据转向基因顺序数据以来,它一直使用各种进化模型进行研究。我们提出了一种基于最大似然和加权最大匹配算法的灵活祖先重建模型FARM来推断祖先基因顺序。这将适应各种进化场景,不仅包括基因组重排,还包括插入/删除(indels),片段复制和全基因组复制。我们通过各种模拟进化实验来评估这项工作,并将FARM与现有方法(如InferCarsPro, GASTS和pma++)进行比较。FARM在运行时间和最终组装过程上有显著改善,因此可以用于大规模真实生物数据的祖先推断。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信