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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