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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.

SUBMITTER: Graber JH

PROVIDER: S-EPMC113205 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature

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

Graber Joel H JH McAllister Gregory D GD Smith Temple F TF

Nucleic acids research 20020401 8

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 seq ...[more]

PMID: 11937640

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