Assessing diversity of DNA structure-related sequence features in prokaryotic genomes.

ABSTRACT: Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the DNA molecule. We present a survey of local sequence patterns which have a potential to promote non-canonical DNA conformations (i.e. different from standard B-DNA double helix) and interpret the results in terms of relationships with organisms' habitats, phylogenetic classifications, and other characteristics. Our present work differs from earlier similar surveys not only by investigating a wider range of sequence patterns in a large number of genomes but also by using a more realistic null model to assess significant deviations. Our results show that simple sequence repeats and Z-DNA-promoting patterns are

SUBMITTER: Huang Y 

PROVIDER: S-EPMC4060949 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature