Clustering of identical oligomers in coding and noncoding DNA sequences

We develop a quantitative method for analyzing repetitions of identical sho rt oligomers in coding and noncoding DNA sequences. We analyze sequences pr esently available in the GenBank separately for primate, mammal, vertebrate , rodent, invertebrate and plant taxonomic partitions. We find that some ol igomers "cluster" more than they would if randomly distributed, while other oligomers "repel" each other. To quantify this degree of clustering, we de fine clustering measures. We find that (i) clustering significantly differs in coding and noncoding DNA; (ii) in most cases, monomers, dimers and tetr amers cluster in noncoding DNA but appear to repel each other in coding DNA . (iii) The degree of clustering for different sources (primates, invertebr ates, and plants) is more conserved among these sources in the case of codi ng DNA than in the case of noncoding DNA. (iv) In contrast to other oligome rs, we find that trimers always prefer to cluster. (v) Clustering of each p articular oligomer is conserved within the same organism.