Accurate splice site prediction using support vector machines

BackgroundFor 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.ResultsIn 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.AvailabilityData, splits, additional information on the model selection, the whole genome predictions, as well as the stand-alone prediction tool are available for download at http://www.fml.mpg.de/raetsch/projects/splice.

• Publication year

  2007

• Venue

  BMC Bioinformatics

• Publication date

  2007-12-21

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-8-S10-S7PMID 18269701PMCID 2230508
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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