Quantitative analysis and assessment of base composition asymmetry and gene orientation bias in bacterial genomes. Issue 9 (11th April 2019)

• Record Type: Journal Article
• Authors: Quan, Chun‐Lan; Gao, Feng
• Is Part Of: FEBS letters. Volume 593:Issue 9(2019)
• Page Start: 918
• Page End: 925
• Publication Date: 2019-04-11
• Subjects: correlation coefficient -- gene orientation bias -- base composition asymmetry -- the Z‐curve method; Biochemistry -- Periodicals; Biophysics -- Periodicals; Molecular biology -- Periodicals; Biochimie -- Périodiques; Biochemistry; Biophysics; Molecular biology; Periodicals; 572.05
• DOI: 10.1002/1873-3468.13374
• Languages: English
• ISSNs: 0014-5793

Abstract

Abstract : 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 R 2 is used for evaluation. We find that skew curves with higher R 2 perform better on the prediction of replication origins in bacteria. Abstract :