{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T01:41:59Z","timestamp":1775958119296,"version":"3.50.1"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T00:00:00Z","timestamp":1654646400000},"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\/501100010096","name":"Southern Medical University","doi-asserted-by":"publisher","award":["G618289088"],"award-info":[{"award-number":["G618289088"]}],"id":[{"id":"10.13039\/501100010096","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,18]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The identification of the conserved and variable regions in the multiple sequence alignment (MSA) is critical to accelerating the process of understanding the function of genes. MSA visualizations allow us to transform sequence features into understandable visual representations. As the sequence\u2013structure\u2013function relationship gains increasing attention in molecular biology studies, the simple display of nucleotide or protein sequence alignment is not satisfied. A more scalable visualization is required to broaden the scope of sequence investigation. Here we present ggmsa, an R package for mining comprehensive sequence features and integrating the associated data of MSA by a variety of display methods. To uncover sequence conservation patterns, variations and recombination at the site level, sequence bundles, sequence logos, stacked sequence alignment and comparative plots are implemented. ggmsa supports integrating the correlation of MSA sequences and their phenotypes, as well as other traits such as ancestral sequences, molecular structures, molecular functions and expression levels. We also design a new visualization method for genome alignments in multiple alignment format to explore the pattern of within and between species variation. Combining these visual representations with prime knowledge, ggmsa assists researchers in discovering MSA and making decisions. The ggmsa package is open-source software released under the Artistic-2.0 license, and it is freely available on Bioconductor (https:\/\/bioconductor.org\/packages\/ggmsa) and Github (https:\/\/github.com\/YuLab-SMU\/ggmsa).<\/jats:p>","DOI":"10.1093\/bib\/bbac222","type":"journal-article","created":{"date-parts":[[2022,5,11]],"date-time":"2022-05-11T11:42:13Z","timestamp":1652269333000},"source":"Crossref","is-referenced-by-count":212,"title":["ggmsa: a visual exploration tool for multiple sequence alignment and associated data"],"prefix":"10.1093","volume":"23","author":[{"given":"Lang","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"},{"name":"Division of Laboratory Medicine, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University , Guangzhou, China"}]},{"given":"Tingze","family":"Feng","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"}]},{"given":"Shuangbin","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"}]},{"given":"Fangluan","family":"Gao","sequence":"additional","affiliation":[{"name":"Institute of Plant Virology, Fujian Agriculture and Forestry University , Fuzhou, China"}]},{"given":"Tommy T","family":"Lam","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong , Hong Kong SAR, China"},{"name":"Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks , Hong Kong SAR, China"}]},{"given":"Qianwen","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"},{"name":"Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China"}]},{"given":"Tianzhi","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"}]},{"given":"Huina","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"},{"name":"Zhuhai International Travel Healthcare Center , Zhuhai, Guangdong, China"}]},{"given":"Li","family":"Zhan","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"}]},{"given":"Lin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"}]},{"given":"Yi","family":"Guan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong , Hong Kong SAR, China"},{"name":"Joint Institute of Virology (Shantou University - The University of Hong Kong), Shantou University , Shantou, China"}]},{"given":"Zehan","family":"Dai","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6485-8781","authenticated-orcid":false,"given":"Guangchuang","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China"},{"name":"Division of Laboratory Medicine, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University , 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