New methods for splice site recognition

Abstract. Splice sites are locations in DNA which separate protein-coding regions (ex-ons) from noncoding regions (introns). Accurate splice site detectors thus form important components of computational gene finders. We pose splice site recognition as a classifi-cation problem with the classifier learnt from a labeled data set consisting of only local information around the potential splice site. Note that finding the correct position of splice sites without using global information is a rather hard task. We analyze the genomes of the nematode Caenorhabditis elegans and of humans using specially designed support vector kernels. One of the kernels is adapted from our previous work on detecting translation ini-tiation sites in vertebrates and another uses an extension to the well-known Fisher-kernel. We find excellent performance on both data sets.