Extensive search for discriminative features of alternative splicing

Alternative pre-mRNA splicing events can be classified into various types, including cassette, mutually exclusive, alternative 3' splice site, alternative 5' splice site, retained intron. The detection of features of a particular type of alternative splicing events is an important and challenging problem in understanding the mechanism of alternative splicing. In this paper, we consider the problem of finding regulatory sequence patterns, which are specific to a particular type of alternative splicing events, on alternative exons and their flanking introns. For this problem, we have designed various pattern features and evaluated them on the alternative splicing data compiled in Lee's ASAP (Alternative Splicing Annotation Project) database. Through our work, we have succeeded in finding features with practically high accuracies.