Features generated for computational splice-site prediction correspond to functional elements

Background: Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA) that is capable of achieving high classification accuracy on human 3' splice sites. In this paper, we extend the splice-site prediction to 5' splice sites and explore the generated features for biologically meaningful splicing signals. Results: We present examples from the observed features that correspond to known signals, both core signals (including the branch site and pyrimidine tract) and auxiliary signals (including GGG triplets and exon splicing enhancers). We present evidence that features identified by FGA include splicing signals not found by other methods. Conclusion: Our generated features capture known biological signals in the expected sequence interval flanking splice sites. Th...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount
• Keywords: BMCBI 2007, Meaningful Splicing Signals, Splice Sites, Splicing Signals