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Quantitative analysis and assessment of base composition asymmetry and gene orientation bias in bacterial genomes
Author(s) -
Quan ChunLan,
Gao Feng
Publication year - 2019
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1002/1873-3468.13374
Subject(s) - skew , genome , bacterial genome size , asymmetry , biology , genetics , gene , gc content , computational biology , physics , quantum mechanics , astronomy
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.