Quantitative analysis and assessment of base composition asymmetry and gene orientation bias in bacterial genomes

FEBS Lett. 2019 May;593(9):918-925. doi: 10.1002/1873-3468.13374. Epub 2019 Apr 11.


Base composition asymmetry and gene orientation bias are two common genomic structures in bacterial genomes. Here, correlation coefficients between nucleotide disparities and coding sequence (CDS) skew have been calculated, which provides insights into their relationship from an individual genome perspective. Consequently, we find GC and RY disparities correlate significantly with CDS skew, since around 60% of the bacterial genomes under study have correlation coefficients > 0.9. Then, we present a model for quantitative assessment of nucleotide disparity and CDS skew in which a numerical index R2 is used for evaluation. We find that skew curves with higher R2 perform better on the prediction of replication origins in bacteria.

Keywords: base composition asymmetry; correlation coefficient; gene orientation bias; the Z-curve method.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Genome, Bacterial / genetics*
  • Genomics
  • Models, Genetic
  • Nucleotides / genetics


  • Nucleotides