Computational Analysis of the Distribution of Short Repeated Motifs in Human Genomic Sequences

Over the last several years the search for functional elements in human and other genomes by exploiting motif over-representation became increasingly popular. However, about half of the human genome consists of known repeated elements, and that is also the case with most higher eukaryotes. In this study we have shown that in addition to these known repeats, human genomic sequence features many short motifs which are significantly over-represented, and that their frequency varies only slightly between random repeat–masked sequences and regions located immediately upstream of the known genes. As the ongoing ENCODE project is set on the development of the techniques for high–throughput identification of the functional elements in the human genome, concentrating on about 1% of its entire DNA sequence, we have chosen these regions for a part of our study.