Prototype Based Recognition of Splice Sites

Abstract

Splice site recognition is an important subproblem of de novo gene finding, splice junctions constituting the boundary between coding and non-coding regions in eukaryotic DNA. The availability of large amounts of sequenced DNA makes the development of fast and reliable tools for automatic identi.cation of important functional regions of DNA necessary. We present a prototype based pattern recognition tool trained for automatic donor and acceptor recognition. The developed classification model is very sparse and allows fast identification of splice sites. The method is compared with a recent model based on support vector machines on two publicly available data sets, a well known benchmark from the UCIrepository for human DNA [6] and a large dataset containing DNA of C.elegans. Our method shows competitive results and the achieved model is much sparser.¹