Prediction of over represented transcription factor binding sites in co-regulated genes using whole genome matching statistics

important and challenging problems in molecular biology and bioinformatics. Here we present an algorithm that, given a set of promoters from co-regulated genes, identifies over-represented binding sites by using profiles (position specific frequency matrices) defining the sequence binding specificity of known TFs as well as matching statistics on a whole-genome level, bypassing the need of defining matching thresholds and/or the use of homologous sequences. Preliminary tests performed on experimentally validated sequence sets are very promising; moreover, the same algorithm is suitable also for the use with any model of the binding specificity of TFs.