Mean zscore on 242 complete bacterial chromosomes
This dataset contains the mean zscores as computed on all intergenic sequences (intergenic) and on all CDS (coding) from 242 complete bacterial chromosomes (as retrieved from Genome Reviews database on June 16, 2005).
data(dinucl)
List of two dataframes of 242 chromosomes and 16 dinucleotides: one for intergenic, one for coding sequences.
the mean of zscore computed with the base
model on each intergenic sequence
the mean of zscore computed with the codon
model on each coding sequence
Palmeira, L., Guéguen, L. and Lobry JR. (2006) UV-targeted dinucleotides
are not depleted in light-exposed Prokaryotic genomes.
Molecular Biology and Evolution,
23:2214-2219.
https://academic.oup.com/mbe/article/23/11/2214/1335460
citation("seqinr")
data(dinucl)
par(mfrow = c(2, 2), mar = c(4,4,0.5,0.5)+0.1)
myplot <- function(x){
plot(dinucl$intergenic[, x], dinucl$coding[, x],
xlab = "intergenic", ylab = "coding",
las = 1, ylim = c(-6, 4),
xlim = c(-3, 3), cex = 0)
rect(-10,-10,-1.96,10,col="yellow", border = "yellow")
rect(1.96,-10,10,10,col="yellow", border = "yellow")
rect(-10,-10,10,-1.96,col="yellow", border = "yellow")
rect(-10,1.96,10,10,col="yellow", border = "yellow")
abline(v=0,lty=3)
abline(h=0,lty=3)
abline(h=-1.96,lty=2)
abline(h=+1.96,lty=2)
abline(v=-1.96,lty=2)
abline(v=+1.96,lty=2)
points(dinucl$intergenic[, x], dinucl$coding[, x], pch = 21,
col = rgb(.1,.1,.1,.5), bg = rgb(.5,.5,.5,.5))
legend("bottomright", inset = 0.02,
legend = paste(substr(x,1,1), "p",
substr(x,2,2), " bias", sep = ""), cex = 1.25, bg = "white")
box()
}
myplot("CT")
myplot("TC")
myplot("CC")
myplot("TT")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.