Distance conservation of transcription regulatory motifs in saccharomyces cerevisiae promoters

Through the comparative studies of k-mer distribution in Saccharomyces cerevisiae (S.ce) and Schizosaccharomyces pombe (S.po) transcription factor binding site (TFBS) sequences we have discovered that the average distance between a pair of transcription regulatory 7-mer motifs is conservative in S.ce-S.po promoters. The distance conservation is a new kind of evolutionary conservation, not based on the strict location of bases in genome sequence. By utilizing the conservation of k-mer distance it will be helpful to propose a non-alignment-based approach for fast discovery of transcription regulatory motifs in genome-wide. We demonstrated the distance conservation by genome-wide searching of conservative regulatory 7-mer motifs with successful rate: sensitivity 78%, specificity 77% and correlation coefficient 0.49.