Evolving Core Promoter Signal Motifs

DNA annotation is an important problem in molecular biology. The task in annotation is to detrmine functional roles of DNA regions. In this article, we are interested in core promoter regions in eukaryotes; these are approximately 50bp in length, and are believed to act as the critical factor in attracting the transcription initiation complex to the DNA at that Site, so promoting the transcription of a gene immediately downstream. The pattern of nucleotides which constitute a core promoter region is very complex, resulting in relatively poor performance from classification methods so far in terms of distinguishing true core promoter regions from other regions of DNA. The methods we describe here both use evolutionary algorithms to optimise simple models of core promoter regions. They seem to perform comparably to the best of many published methods so far, but has the advantage of simplicity and transparency. That is, we are able to evolve easily understandable models of the core promoter region which perform comparably with the best of existing techniques. There seem to be several ways in which the scheme can be further developed.