The Study Of Strand Compositional Bias And Its Underlying Mechanism In Bacterial Genomes

The rapid development of high-throughput sequencing technology has produced a huge amount of genomic data.How to use these data to mine meaningful biological information has become new opportunities as well as challenges for bioinformatic in the era of big data.As a very important component of the microbial population,bacteria are closely related to human life.The understanding of bacterial genomes can make bacteria play a better role in the fields of medicine,environmental protection,biotechnology and so on.There are different replication mechanisms between the leading and lagging strands during DNA replication.Former studies indicate that the majority of bacterial genomes display base composition asymmetry and gene orientation bias.First of all,we have calculated the correlation coefficients between nucleotide disparities and CDS(coding sequence)skew,which provides new insights into their relationship from an individual genome perspective.Consequently,we find GC and RY disparities correlate significantly with CDS skew since around 60%bacterial genomes under study have the correlation coefficients greater than 0.9.Moreover,to assess nucleotide disparity and CDS skew,an algorithm has been developed based on the V shape model,which is evaluated with R~2 for the goodness of fit.In general,both base composition asymmetry and gene orientation bias can be used to detect replication origins in bacteria.Among them,GC disparity is the most common one for predicting the origins of replication in silico,but fluctuating GC disparity also occurs in some bacterial genomes.For these genomes,other clear-cut disparities with high R~2,such as AT disparity,CDS skew,could be considered to identify the replication origins more precisely.