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Nucleic Acids Research, 2002, Vol. 30, No. 8 1851-1858
© 2002 Oxford University Press

Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites

Joel H. Graber1,3,*, Gregory D. McAllister2,3 and Temple F. Smith2,3

1Center for Advanced Biotechnology and 2Biomolecular Engineering Research Center, Boston University, 36 Cummington Street, Boston, MA 02215, USA and 3Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA

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.

* To whom correspondence should be addressed at present address: Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA. Tel: +1 617 358 2506; Fax: +1 617 353 4814; Email: jhgraber{at}bu.edu


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