{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,26]],"date-time":"2026-01-26T13:49:23Z","timestamp":1769435363653,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2022,7,22]],"date-time":"2022-07-22T00:00:00Z","timestamp":1658448000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Hong Kong Research Grants Council Area of Excellence Scheme","award":["AoE\/M-403\/16"],"award-info":[{"award-number":["AoE\/M-403\/16"]}]},{"name":"Lo Kwee-Seong Biomedical Research Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Synteny analysis is a widely used framework in comparative genomics studies, which provides valuable information to reveal chromosome collinearity in both intra-species and inter-species. Most analysis pipelines, however, are command line-based, making it challenging for biologists to run the algorithms and visualize the results. Existing visualization tools either provide static plots or can only be run on web-based servers and lack efficient visualization methods for associating macro-synteny blocks with individual gene pairs in a micro-synteny region.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed ShinySyn, a Shiny\/R application built on the MCscan framework that provides an easy-to-use graphic interface for synteny analyses without requiring any programming skills, to reduce technical barriers. ShinySyn not only provides interactive visualization for macro-synteny, micro-synteny and genome-level dot views, but it also creates an intuitive representation with a dynamic zooming feature from macro-synteny to individual homologous genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The source code and installation instructions for ShinySyn can be accessed via https:\/\/github.com\/obenno\/ShinySyn. A pre-built docker image is also available at https:\/\/hub.docker.com\/r\/obenno\/shinysyn. The application can be used locally or seamlessly integrated into any Shiny application server.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac503","type":"journal-article","created":{"date-parts":[[2022,7,22]],"date-time":"2022-07-22T12:19:09Z","timestamp":1658492349000},"page":"4406-4408","source":"Crossref","is-referenced-by-count":21,"title":["ShinySyn: a Shiny\/R application for the interactive visualization and integration of macro- and micro-synteny data"],"prefix":"10.1093","volume":"38","author":[{"given":"Zhixia","family":"Xiao","sequence":"first","affiliation":[{"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, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6673-8740","authenticated-orcid":false,"given":"Hon-Ming","family":"Lam","sequence":"additional","affiliation":[{"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, China"}]}],"member":"286","published-online":{"date-parts":[[2022,7,22]]},"reference":[{"key":"2023041408240393100_","author":"Attali","year":"2021"},{"key":"2023041408240393100_","first-page":"74","author":"Bandi","year":"2020"},{"key":"2023041408240393100_","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","article-title":"TBtools: an integrative toolkit developed for interactive analyses of big biological data","volume":"13","author":"Chen","year":"2020","journal-title":"Mol. 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