Clustering of identical oligomers in coding and noncoding dna sequences

Rachel H.R. Stanley, Nikolay V. Dokholyan, Sergey V. Buldyrev, Shlomo Havlin, H. Eugene Stanley

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)79-87
Number of pages9
JournalJournal of Biomolecular Structure and Dynamics
Issue number1
StatePublished - Aug 1999

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology


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