@article{SonSchPhiBehRae07, author = {S\"oren Sonnenburg and Gabriele Schweikert and Petra Philips and Jonas Behr and Gunnar R\"atsch}, title = {{Accurate Splice Site Prediction}}, journal = {BMC Bioinformatics, Special Issue from NIPS workshop on New Problems and Methods in Computational Biology Whistler, Canada, 18 December 2006}, year = 2007, month = {December}, volume = 8, pages = {(Suppl. 10):S7}, pdf = {http://www.biomedcentral.com/1471-2105/8/S10/S7}, dataset = {http://www.fml.tuebingen.mpg.de/raetsch/projects/splice}, abstract = {Background: For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks. Results: In this work we consider Support Vector Machines for splice site recognition. We employ the so-called weighted degree kernel which turns out well suited for this task, as we will illustrate in several experiments where we compare its prediction accuracy with that of recently proposed systems. We apply our method to the genome-wide recognition of splice sites in Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio, and Homo sapiens. Our performance estimates indicate that splice sites can be recognized very accurately in these genomes and that our method outperforms many other methods including Markov Chains, GeneSplicer and SpliceMachine. We provide genome-wide predictions of splice sites and a stand-alone prediction tool ready to be used for incorporation in a gene finder.} }