title: Prediction of mRNA polyadenylation sites by support vector machine.
abstract: mRNA polyadenylation is responsible for the 3' end formation of most mRNAs in eukaryotic cells and is linked to termination of transcription. Prediction of mRNA polyadenylation sites [poly(A) sites] can help identify genes, define gene boundaries, and elucidate regulatory mechanisms. Current methods for poly(A) site prediction achieve moderate sensitivity and specificity. Here, we present a method using support vector machine for poly(A) site prediction. Using 15 cis-regulatory elements that are over-represented in various regions surrounding poly(A) sites, this method achieves higher sensitivity and similar specificity when compared with polyadq, a common tool for poly(A) site prediction. In addition, we found that while the polyadenylation signal AAUAAA and U-rich elements are primary determinants for poly(A) site prediction, other elements contribute to both sensitivity and specificity of the prediction, indicating a combinatorial mechanism involving multiple elements when choosing poly(A) sites in human cells.
authors.affiliation: Department of Mathematical Sciences, New Jersey Institute of Technology Newark, NJ 07102, USA.
authors.forename: Yiming
authors.initials: Y
authors.lastname: Cheng
authors.forename: Robert M
authors.initials: RM
authors.lastname: Miura
authors.forename: Bin
authors.initials: B
authors.lastname: Tian
mesh_terms: D001185:Artificial Intelligence; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D011061:Poly A / Q000235:genetics*; D026723:Polyadenylation / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger; D011061:Poly A