Prokaryote clustering based on DNA curvature distributions

L. Kozobay-Avraham, S. Hosid, Z. Volkovich, A. Bolshoy

Research output: Contribution to journalArticlepeer-review

Abstract

Massive determination of complete genome sequences has led to the development of different tools for genome comparisons. Our approach is to compare genomes according to typical genomic distributions of a mathematical function that reflects a certain biological function. In this study we used comprehensive genome analysis of DNA curvature distributions in coding and non-coding regions of prokaryotic genomes to evaluate the assistance of mathematical and statistical procedures. Due to an extensive amount of data we were able to define the factors influencing the curvature distribution in promoter and terminator regions such as growth temperature, genome size, and A + T composition. Two clustering methods, K-means and PAM, were applied and produced very similar clusterings that reflect genomic attributes and environmental conditions of the species' habitat.

Original languageEnglish
Pages (from-to)2378-2387
Number of pages10
JournalDiscrete Applied Mathematics
Volume157
Issue number10
DOIs
StatePublished - 28 May 2009

Keywords

  • Clustering methods
  • Curved DNA
  • k-means
  • PAM

ASJC Scopus subject areas

  • Discrete Mathematics and Combinatorics
  • Applied Mathematics

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