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Synonymous recoding of viral genes through codon and codon-pair deoptimization offers a promising approach to design live attenuated vaccines (LAVs) by reducing viral fitness without altering protein sequences. This strategy has been successfully applied to develop vaccines for a range of pathogens affecting human and livestock. To support this approach, we developed CocoVax, the first web server dedicated to codon and codon-pair deoptimization for LAV design. CocoVax features four modules, Virus Database, Gene Recoder, Sequence Evaluator, and Reference Library, guiding users through the entire vaccine development process. With its intuitive interface, CocoVax enables rapid generation of vaccine candidates using only a pathogen\u2019s gene sequence, providing a valuable resource for researchers in virology and vaccine development. CocoVax is freely accessible at https:\/\/comics.med.sustech.edu.cn\/cocovax with no login required.<\/jats:p>","DOI":"10.1093\/nar\/gkaf358","type":"journal-article","created":{"date-parts":[[2025,4,17]],"date-time":"2025-04-17T07:55:30Z","timestamp":1744876530000},"page":"W178-W186","source":"Crossref","is-referenced-by-count":1,"title":["CocoVax: a web server for codon-based deoptimization of viral genes in live attenuated vaccine design"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1782-5784","authenticated-orcid":false,"given":"Jiaxuan","family":"Li","sequence":"first","affiliation":[{"name":"School of Medicine, Southern University of Science and Technology Department of Human Cell Biology and Genetics, , Shenzhen , Guangdong 518055 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9527-8018","authenticated-orcid":false,"given":"Shimin","family":"Shuai","sequence":"additional","affiliation":[{"name":"School of Medicine, Southern University of Science and Technology Department of Human Cell Biology and Genetics, , Shenzhen , Guangdong 518055 ,","place":["China"]},{"name":"SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology , Shenzhen , Guangdong 518055 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,4,29]]},"reference":[{"key":"2025070706165492800_B1","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/j.virol.2015.03.032","article-title":"Live attenuated vaccines: historical successes and current 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