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Eukaryotic pre-mRNAs are spliced to form mature mRNA. Pre-mRNA alternative splicing greatly increases the complexity of gene expression. Estimates show that more than half of the human genes and at least one-third of the genes of less complex organisms, such as nematodes or flies, are alternatively spliced. In this work, we consider one major form of alternative splicing, namely the exclusion of exons from the transcript. It has been shown that alternatively spliced exons have certain properties that distinguish them from constitutively spliced exons. Although most recent computational studies on alternative splicing apply only to exons which are conserved among two species, our method only uses information that is available to the splicing machinery, i.e. the DNA sequence itself. We employ advanced machine learning techniques in order to answer the following two questions: (1) Is a certain exon alternatively spliced? (2) How can we identify yet unidentified exons within known introns?

RASE: recognition of alternatively spliced exons in C.elegans