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

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

Quan CL1, Gao F1,2,3.

Author information

1
Department of Physics, School of Science, Tianjin University, China.
2
Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, China.
3
SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), China.

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 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

PMID:
30941752
DOI:
10.1002/1873-3468.13374

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