{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T11:01:21Z","timestamp":1784804481821,"version":"3.55.0"},"reference-count":143,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T00:00:00Z","timestamp":1646870400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61922020"],"award-info":[{"award-number":["61922020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can reveal the potential information in biological sequences, such as function, evolution and structure. MSA is widely used in many bioinformatics scenarios, such as phylogenetic analysis, protein analysis and genomic analysis. However, MSA faces new challenges with the gradual increase in sequence scale and the increasing demand for alignment accuracy. Therefore, developing an efficient and accurate strategy for MSA has become one of the research hotspots in bioinformatics. In this work, we mainly summarize the algorithms for MSA and its applications in bioinformatics. To provide a structured and clear perspective, we systematically introduce MSA\u2019s knowledge, including background, database, metric and benchmark. Besides, we list the most common applications of MSA in the field of bioinformatics, including database searching, phylogenetic analysis, genomic analysis, metagenomic analysis and protein analysis. Furthermore, we categorize and analyze classical and state-of-the-art algorithms, divided into progressive alignment, iterative algorithm, heuristics, machine learning and divide-and-conquer. Moreover, we also discuss the challenges and opportunities of MSA in bioinformatics. Our work provides a comprehensive survey of MSA applications and their relevant algorithms. It could bring valuable insights for researchers to contribute their knowledge to MSA and relevant studies.<\/jats:p>","DOI":"10.1093\/bib\/bbac069","type":"journal-article","created":{"date-parts":[[2022,2,9]],"date-time":"2022-02-09T20:11:57Z","timestamp":1644437517000},"source":"Crossref","is-referenced-by-count":33,"title":["A survey on the algorithm and development of multiple sequence alignment"],"prefix":"10.1093","volume":"23","author":[{"given":"Yongqing","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"},{"name":"School of Computer Science and Engineering, University of Electronic Science and Technology of China, 611731, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiliu","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Computer Science, Chengdu University of Information Technology, 610225, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 610054, Chengdu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,3,10]]},"reference":[{"issue":"8","key":"2022051813160393700_ref1","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1007\/s10529-020-02914-0","article-title":"Small design from big alignment: engineering proteins with multiple sequence alignment as the starting point","volume":"42","author":"Wang","year":"2020","journal-title":"Biotechnol 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