重排距离问题:最新调查

IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, THEORY & METHODS
Andre Rodrigues Oliveira, Klairton Lima Brito, Alexsandro Oliveira Alexandrino, Gabriel Siqueira, Ulisses Dias, Zanoni Dias
{"title":"重排距离问题:最新调查","authors":"Andre Rodrigues Oliveira, Klairton Lima Brito, Alexsandro Oliveira Alexandrino, Gabriel Siqueira, Ulisses Dias, Zanoni Dias","doi":"10.1145/3653295","DOIUrl":null,"url":null,"abstract":"<p>One of the challenges in the Comparative Genomics field is to infer how close two organisms are based on the similarities and differences between their genetic materials. Recent advances in DNA sequencing have made complete genomes increasingly available. That said, several new algorithms trying to infer the distance between two organisms based on genome rearrangements have been proposed in the literature. However, given the diversity of approaches, the diversity of genome rearrangement events, or even how each work models the genomes and what assumptions are made by each of them, finding the ideal algorithm for each situation or simply knowing the range of applicable approaches can be challenging. In this work, we review these approaches having the algorithmic and combinatorial advances since 2010 as our main focus. This survey aims to organize the recently published papers using a concise notation and to indicate the gaps filled by each of them in the literature. This makes it easier to understand what still needs to be done and what has room for enhancement.</p>","PeriodicalId":50926,"journal":{"name":"ACM Computing Surveys","volume":null,"pages":null},"PeriodicalIF":23.8000,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Rearrangement Distance Problems: An updated survey\",\"authors\":\"Andre Rodrigues Oliveira, Klairton Lima Brito, Alexsandro Oliveira Alexandrino, Gabriel Siqueira, Ulisses Dias, Zanoni Dias\",\"doi\":\"10.1145/3653295\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>One of the challenges in the Comparative Genomics field is to infer how close two organisms are based on the similarities and differences between their genetic materials. Recent advances in DNA sequencing have made complete genomes increasingly available. That said, several new algorithms trying to infer the distance between two organisms based on genome rearrangements have been proposed in the literature. However, given the diversity of approaches, the diversity of genome rearrangement events, or even how each work models the genomes and what assumptions are made by each of them, finding the ideal algorithm for each situation or simply knowing the range of applicable approaches can be challenging. In this work, we review these approaches having the algorithmic and combinatorial advances since 2010 as our main focus. This survey aims to organize the recently published papers using a concise notation and to indicate the gaps filled by each of them in the literature. This makes it easier to understand what still needs to be done and what has room for enhancement.</p>\",\"PeriodicalId\":50926,\"journal\":{\"name\":\"ACM Computing Surveys\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":23.8000,\"publicationDate\":\"2024-03-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACM Computing Surveys\",\"FirstCategoryId\":\"94\",\"ListUrlMain\":\"https://doi.org/10.1145/3653295\",\"RegionNum\":1,\"RegionCategory\":\"计算机科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"COMPUTER SCIENCE, THEORY & METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACM Computing Surveys","FirstCategoryId":"94","ListUrlMain":"https://doi.org/10.1145/3653295","RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"COMPUTER SCIENCE, THEORY & METHODS","Score":null,"Total":0}
引用次数: 0

摘要

比较基因组学领域的挑战之一是根据两种生物遗传物质的异同来推断它们之间的亲缘关系。最近,DNA 测序技术的进步使得越来越多的人可以获得完整的基因组。因此,文献中提出了几种新算法,试图根据基因组重排来推断两种生物之间的距离。然而,由于方法的多样性、基因组重排事件的多样性,甚至每种方法是如何建立基因组模型的,以及每种方法都做了哪些假设,因此要为每种情况找到理想的算法,或者仅仅了解适用方法的范围都具有挑战性。在这项工作中,我们以 2010 年以来的算法和组合进展为重点,对这些方法进行了回顾。本调查旨在使用简洁的符号组织近期发表的论文,并指出每篇论文在文献中填补的空白。这样,我们就能更容易地了解哪些方面还有待改进,哪些方面还有提升的空间。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Rearrangement Distance Problems: An updated survey

One of the challenges in the Comparative Genomics field is to infer how close two organisms are based on the similarities and differences between their genetic materials. Recent advances in DNA sequencing have made complete genomes increasingly available. That said, several new algorithms trying to infer the distance between two organisms based on genome rearrangements have been proposed in the literature. However, given the diversity of approaches, the diversity of genome rearrangement events, or even how each work models the genomes and what assumptions are made by each of them, finding the ideal algorithm for each situation or simply knowing the range of applicable approaches can be challenging. In this work, we review these approaches having the algorithmic and combinatorial advances since 2010 as our main focus. This survey aims to organize the recently published papers using a concise notation and to indicate the gaps filled by each of them in the literature. This makes it easier to understand what still needs to be done and what has room for enhancement.

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
ACM Computing Surveys
ACM Computing Surveys 工程技术-计算机:理论方法
CiteScore
33.20
自引率
0.60%
发文量
372
审稿时长
12 months
期刊介绍: ACM Computing Surveys is an academic journal that focuses on publishing surveys and tutorials on various areas of computing research and practice. The journal aims to provide comprehensive and easily understandable articles that guide readers through the literature and help them understand topics outside their specialties. In terms of impact, CSUR has a high reputation with a 2022 Impact Factor of 16.6. It is ranked 3rd out of 111 journals in the field of Computer Science Theory & Methods. ACM Computing Surveys is indexed and abstracted in various services, including AI2 Semantic Scholar, Baidu, Clarivate/ISI: JCR, CNKI, DeepDyve, DTU, EBSCO: EDS/HOST, and IET Inspec, among others.
×
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