title: Clustering of identical oligomers in coding and noncoding DNA sequences.
abstract: We develop a quantitative method for analyzing repetitions of identical short oligomers in coding and noncoding DNA sequences. We analyze sequences presently available in the GenBank separately for primate, mammal, vertebrate, rodent, invertebrate and plant taxonomic partitions. We find that some oligomers "cluster" more than they would if randomly distributed, while other oligomers "repel" each other. To quantify this degree of clustering, we define clustering measures. We find that (i) clustering significantly differs in coding and noncoding DNA; (ii) in most cases, monomers, dimers and tetramers cluster in noncoding DNA but appear to repel each other in coding DNA. (iii) The degree of clustering for different sources (primates, invertebrates, and plants) is more conserved among these sources in the case of coding DNA than in the case of noncoding DNA. (iv) In contrast to other oligomers, we find that trimers always prefer to cluster. (v) Clustering of each particular oligomer is conserved within the same organism.
authors.affiliation: Center for Polymer Studies and Physics Dept., Boston University, MA 02215, USA.
authors.forename: R H
authors.initials: RH
authors.lastname: Stanley
authors.forename: N V
authors.initials: NV
authors.lastname: Dokholyan
authors.forename: S V
authors.initials: SV
authors.lastname: Buldyrev
authors.forename: S
authors.initials: S
authors.lastname: Havlin
authors.forename: H E
authors.initials: HE
authors.lastname: Stanley
mesh_terms: D000818:Animals; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D005091:Exons; D007438:Introns; D008433:Mathematics; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D009838:Oligodeoxyribonucleotides; D004247:DNA