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

Document Type


Publication Date



Base-Sequence, Comparative-Study, Genes-Fungal, Markov-Chains, RNA-3'-End-Processing, RNA-Fungal, RNA-Messenger, Saccharomyces-cerevisiae, Sensitivity-and-Specificity, SUPPORT-NON-U-S-GOVT, SUPPORT-U-S-GOVT-NON-P-H-S, SUPPORT-U-S-GOVT-P-H-S

JAX Source

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


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 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.