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Nucleic Acids Res. 2002 Apr 15;30(8):1851-8.

Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites.

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  • 1Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA. jhgraber@bu.edu


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.

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