title: Prediction of plant mRNA polyadenylation sites.
abstract: Messenger RNA polyadenylation is one of the essential processing steps during eukaryotic gene expression. The site of polyadenylation [poly(A) site] marks the end of a transcript, which is also the end of a gene in most cases. A computation program that is able to recognize poly(A) sites would not only be useful for genome annotation in finding genes ends, but also for predicting alternative poly(A) sites. PASS [Poly(A) Site Sleuth] and PAC [Poly(A) site Classifier] were developed to predict poly(A) sites in plants. PASS was built based on the Generalized Hidden Markov Model (GHMM), which consists of four functional modules: input model, poly(A) site recognition module, graphic process module, and output module. PAC is a classification model, integrating several features that define the poly(A) sites including K-gram pattern, Z-curve, position-specific scoring matrix, and first-order inhomogeneous Markov sub-model. PAC can be used to predict poly(A) sites from species whose polyadenylation profile is unknown. The result of PASS and PAC is an output of a few files with one of them containing the score or probability of being a poly(A) site for each position of a given sequence. While the models were built mostly based on poly(A) profile data from Arabidopsis, it is also functional in other higher plants since their profiles are quite similar.
authors.affiliation: Department of Automation, Xiamen University, 422 Siming South Road, Xiamen, Fujian, 361005, China, xhuister@xmu.edu.cn.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Wu
authors.forename: Guoli
authors.initials: G
authors.lastname: Ji
authors.forename: Qingshun Quinn
authors.initials: QQ
authors.lastname: Li
mesh_terms: D017360:Arabidopsis / Q000378:metabolism; D019295:Computational Biology; D010944:Plants / Q000378:metabolism*; D011061:Poly A / Q000235:genetics / Q000378:metabolism*; D026723:Polyadenylation; D012333:RNA, Messenger / Q000378:metabolism*; D018749:RNA, Plant / Q000378:metabolism*; D012984:Software
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant; D011061:Poly A