title: Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites.
abstract: We present a tool for the prediction of mRNA 3'-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3'-processing sites indicates good agreement. All predicted or known yeast genes were analyzed to find probable 3'-processing sites. Known alternative 3'-processing sites, both within the 3'-untranslated region and within the protein coding sequence were successfully identified, leading to the possibility of prediction of previously unknown alternative sites. The lack of an apparent 3'-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences.
authors.affiliation: Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA. jhgraber@bu.edu
authors.forename: Joel H
authors.initials: JH
authors.lastname: Graber
authors.forename: Gregory D
authors.initials: GD
authors.lastname: McAllister
authors.forename: Temple F
authors.initials: TF
authors.lastname: Smith
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D005800:Genes, Fungal; D008390:Markov Chains; D026721:RNA 3' End Processing; D012331:RNA, Fungal / Q000032:analysis*; D012333:RNA, Messenger / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D020413:3' Untranslated Regions; D012331:RNA, Fungal; D012333:RNA, Messenger