REGULATORY GENOMIC SEQUENCES PHYLOGENETIC FOOTPRINT. A NEW METHOD FOR PROMOTER ALIGNMENT

Motivation: Phylogenetic Footprint is a new approach for revealing potential transcription factor binding sites in promoter sequences. The idea is based on an assumption that functional sites in promoters should evolve much slower then other regions that do not bear any conservative function. Therefore, potential transcription factor (TF) binding sites that are found in the evolutionally conservative regions of promoters have more chances to be considered as real sites. The most difficult step of the Phylogenetic Footprint is alignment of promoter sequences between different organisms (f.e. human and mouse). The conventional alignment methods often can not align promoters due to the high level of sequence variability. Results: We have developed a new alignment method that takes into account similarity in distribution of potential binding sites. This method has been used effectively for promoter alignment and for revealing new potential binding sites for various transcription factors. We have developed a database of predicted potential TF binding sites in human genome by analyzing human/mouse conserved non-coding sequences (CNS)