识别复制和横向基因转移同时和快速。

IF 0.9 4区生物学 Q4 MATHEMATICAL & COMPUTATIONAL BIOLOGY Journal of Bioinformatics and Computational Biology Pub Date : 2022-02-01 Epub Date: 2021-12-09 DOI:10.1142/S0219720021500335

Zhi-Zhong Chen, Fei Deng, Lusheng Wang

{"title":"识别复制和横向基因转移同时和快速。","authors":"Zhi-Zhong Chen, Fei Deng, Lusheng Wang","doi":"10.1142/S0219720021500335","DOIUrl":null,"url":null,"abstract":"This paper deals with the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications and lateral gene transfers (LGTs) for a given species tree [Formula: see text] and a given gene tree [Formula: see text]. Previously, [Tofigh A, Hallett M, Lagergren J, Simultaneous identification of duplications and lateral gene transfers, IEEE/ACM Trans Comput Biol Bioinf 517-535, 2011.] gave a fixed-parameter algorithm for this problem that runs in [Formula: see text] time, where [Formula: see text] is the number of vertices in [Formula: see text], [Formula: see text] is the number of vertices in [Formula: see text], and [Formula: see text] is the minimum cost of an LCA-reconciliation between [Formula: see text] and [Formula: see text]. In this paper, by refining their algorithm, we obtain a new one for the same problem that finds and outputs the solutions in a compact form within [Formula: see text] time. In the most interesting case where [Formula: see text], our algorithm is [Formula: see text] times faster.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":null,"pages":null},"PeriodicalIF":0.9000,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Identifying duplications and lateral gene transfers simultaneously and rapidly.\",\"authors\":\"Zhi-Zhong Chen, Fei Deng, Lusheng Wang\",\"doi\":\"10.1142/S0219720021500335\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"This paper deals with the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications and lateral gene transfers (LGTs) for a given species tree [Formula: see text] and a given gene tree [Formula: see text]. Previously, [Tofigh A, Hallett M, Lagergren J, Simultaneous identification of duplications and lateral gene transfers, IEEE/ACM Trans Comput Biol Bioinf 517-535, 2011.] gave a fixed-parameter algorithm for this problem that runs in [Formula: see text] time, where [Formula: see text] is the number of vertices in [Formula: see text], [Formula: see text] is the number of vertices in [Formula: see text], and [Formula: see text] is the minimum cost of an LCA-reconciliation between [Formula: see text] and [Formula: see text]. In this paper, by refining their algorithm, we obtain a new one for the same problem that finds and outputs the solutions in a compact form within [Formula: see text] time. In the most interesting case where [Formula: see text], our algorithm is [Formula: see text] times faster.\",\"PeriodicalId\":48910,\"journal\":{\"name\":\"Journal of Bioinformatics and Computational Biology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.9000,\"publicationDate\":\"2022-02-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Bioinformatics and Computational Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1142/S0219720021500335\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2021/12/9 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q4\",\"JCRName\":\"MATHEMATICAL & COMPUTATIONAL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Bioinformatics and Computational Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1142/S0219720021500335","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2021/12/9 0:00:00","PubModel":"Epub","JCR":"Q4","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

本文讨论了给定物种树[公式:见文本]和给定基因树[公式:见文本]中涉及基因复制和横向基因转移(lgt)的所有最小成本lca调和的枚举问题。[J]，王晓明，王晓明，等。基因克隆与基因转移的研究进展[J] .中国生物医学工程学报，2016,33(5):557 - 557。给出了一个固定参数的算法，该算法在[公式:见文]时间内运行，其中[公式:见文]是[公式:见文]中的顶点数，[公式:见文]是[公式:见文]中的顶点数，[公式:见文]是[公式:见文]和[公式:见文]之间lca调和的最小代价。在本文中，通过改进他们的算法，我们得到了一个新的算法，可以在[公式:见文]时间内找到并输出紧凑形式的解。在最有趣的情况下，我们的算法比[Formula: see text]快1倍。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

Identifying duplications and lateral gene transfers simultaneously and rapidly.

This paper deals with the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications and lateral gene transfers (LGTs) for a given species tree [Formula: see text] and a given gene tree [Formula: see text]. Previously, [Tofigh A, Hallett M, Lagergren J, Simultaneous identification of duplications and lateral gene transfers, IEEE/ACM Trans Comput Biol Bioinf 517-535, 2011.] gave a fixed-parameter algorithm for this problem that runs in [Formula: see text] time, where [Formula: see text] is the number of vertices in [Formula: see text], [Formula: see text] is the number of vertices in [Formula: see text], and [Formula: see text] is the minimum cost of an LCA-reconciliation between [Formula: see text] and [Formula: see text]. In this paper, by refining their algorithm, we obtain a new one for the same problem that finds and outputs the solutions in a compact form within [Formula: see text] time. In the most interesting case where [Formula: see text], our algorithm is [Formula: see text] times faster.

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

Journal of Bioinformatics and Computational Biology MATHEMATICAL & COMPUTATIONAL BIOLOGY-

CiteScore

2.10

自引率

0.00%

发文量

期刊介绍： The Journal of Bioinformatics and Computational Biology aims to publish high quality, original research articles, expository tutorial papers and review papers as well as short, critical comments on technical issues associated with the analysis of cellular information. The research papers will be technical presentations of new assertions, discoveries and tools, intended for a narrower specialist community. The tutorials, reviews and critical commentary will be targeted at a broader readership of biologists who are interested in using computers but are not knowledgeable about scientific computing, and equally, computer scientists who have an interest in biology but are not familiar with current thrusts nor the language of biology. Such carefully chosen tutorials and articles should greatly accelerate the rate of entry of these new creative scientists into the field.