Polyadenylation site prediction using interesting emerging patterns

This paper presents a study on polyadenylation site prediction in mRNA sequences. We describe a method, called PolyA-EP, that we developed for predicting polyadenylation sites and we present a systematic study of the problem of recognizing mRNA 3´ ends which contain a polyadenylation site using the proposed method. PolyA-EP exploits the advantages of emerging patterns, namely high understandability and discriminating power and can be used for both descriptive and predictive analysis. In particular, PolyA-EP is a parameterizable tool that can be used in order to extract interesting emerging patterns for describing or predicting polyadenylation sites. Moreover, the extracted emerging patterns can span across many elements around the polyadenylation site. We discuss the results of the experiments we conducted with Arabidopsis thaliana sequences drawing important conclusions and finally we propose a framework that improves the accuracy of polyadenylation site prediction.