Combining frequency and positional information to predict transcription factor binding sites

Motivation: Even though a number of genome projects have been finished on t he sequence level, still only a small proportion of DNA regulatory elements have been identified. Growing amounts of gene expression data provide the possibility of finding coregulated genes by clustering methods. By analysis of the promoter regions of those genes, rather weak signals of transcripti on factor binding sites may be detected. Results: We introduce the new algorithm ITB, an Integrated Tool for Box fin ding, which combines frequency and positional information to predict transc ription factor binding sites in upstream regions of coregulated genes. Moti fs are extracted by exhaustive analysis of regular expression-like patterns and by estimating probabilities of positional clusters of motifs. ITB dete cts consensus sequences of experimentally verified transcription factor bin ding sites of the yeast Saccharomyces cerevisiae. Moreover, a number of new binding site candidates with significant scores are predicted. Besides app lying ITB on yeast upstream regions, the program is run on human promoter s equences.