Explicit alternative splicing prediction
Sorek et al. looked at cassette exons in human and mouse and found a striking pattern of increased intron conservation distinct from constitutive exons [13]. A list of features were compiled including exon length, sequence conservation and k-mer counts [14,15], which were used in a support vector machine (SVM) [15] to classify cassette and constitutive exons. Yeo et al. developed a regularized least-squares classifier, called ACESCAN [16], to identify cassette exons in human/mouse orthologs using a similar feature set. A SVM cassette exon classifier was developed for Caenorhabditis elegans using only single species features and was extended to predict cassette exons in intron sequence [17]. Drosophila melanogaster exons matched to Drosophila pseudoobscura orthologs with conserved flanking intron sequence were observed by Philipps et al. to be enriched for alternatively spliced exons [18].