title: VAAPA: a web platform for visualization and analysis of alternative polyadenylation.
abstract: Polyadenylation [poly(A)] is an essential process during the maturation of most mRNAs in eukaryotes. Alternative polyadenylation (APA) as an important layer of gene expression regulation has been increasingly recognized in various species. Here, a web platform for visualization and analysis of alternative polyadenylation (VAAPA) was developed. This platform can visualize the distribution of poly(A) sites and poly(A) clusters of a gene or a section of a chromosome. It can also highlight genes with switched APA sites among different conditions. VAAPA is an easy-to-use web-based tool that provides functions of poly(A) site query, data uploading, downloading, and APA sites visualization. It was designed in a multi-tier architecture and developed based on Smart GWT (Google Web Toolkit) using Java as the development language. VAAPA will be a valuable addition to the community for the comprehensive study of APA, not only by making the high quality poly(A) site data more accessible, but also by providing users with numerous valuable functions for poly(A) site analysis and visualization.
authors.affiliation: Department of Automation, Xiamen University, Xiamen 361005, Fujian, China.
authors.forename: Jinting
authors.initials: J
authors.lastname: Guan
authors.affiliation: Department of Automation, Xiamen University, Xiamen 361005, Fujian, China.
authors.forename: Jingyi
authors.initials: J
authors.lastname: Fu
authors.affiliation: Department of Automation, Xiamen University, Xiamen 361005, Fujian, China.
authors.forename: Mingcheng
authors.initials: M
authors.lastname: Wu
authors.affiliation: Department of Automation, Xiamen University, Xiamen 361005, Fujian, China.
authors.forename: Longteng
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Automation, Xiamen University, Xiamen 361005, Fujian, China; Innovation Center for Cell Biology, Xiamen University, Xiamen 361102, Fujian, China.
authors.forename: Guoli
authors.initials: G
authors.lastname: Ji
authors.affiliation: Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, and College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China; Department of Biology, Miami University, Oxford, OH 45056, USA.
authors.forename: Qingshun
authors.initials: Q
authors.lastname: Quinn Li
authors.affiliation: Department of Automation, Xiamen University, Xiamen 361005, Fujian, China. Electronic address: xhuister@xmu.edu.cn.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Wu
mesh_terms: D000818:Animals; D017360:Arabidopsis; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D020407:Internet; D051379:Mice; D008957:Models, Genetic; D011061:Poly A; D026723:Polyadenylation; D012333:RNA, Messenger / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D011061:Poly A
keywords: Alternative polyadenylation; Poly(A) cluster; Poly(A) site; Poly(A) tag; Web platform