The work most similar to the model introduced in this article is the pair-HMM UNCOVER [23], which finds exons in sequence annotated as introns and was tested on human/mouse intron pairs. Unlike the cassette exon classification methods [15-17], models were trained using examples of protein coding exons without explicitly distinguishing between constitutive exons and cassette exons. Since the input sequence is assumed to be an intron, predicted exons are inferred to be alternatively spliced.