An exploration into improving DNA motif inference by looking for highly conserved core regions

Although most verified functional elements in non-coding DNA contain a highly conserved core region, this concept is not generally incorporated into de novo motif inference systems. In this work, we explore the utility of adding the notion of conserved core regions into a comparative genomics approach for the search for putative functional elements in noncoding DNA. By modifying the scoring function for GAMI, Genetic Algorithms for Motif Inference, we investigate tradeoffs between the strength of conservation of the full motif vs. the strength of conservation of a core region. This work illustrates that incorporating information about the structure of transcription factor binding sites can be helpful in identifying biologically functional elements.