seqinr (version 3.1-2)

dinucl: Mean zscore on 242 complete bacterial chromosomes

Description

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).

Usage

data(dinucl)

encoding

latin1

References

Palmeira, L., Gu�guen, L. and Lobry JR. (2006) UV-targeted dinucleotides are not depleted in light-exposed Prokaryotic genomes. Molecular Biology and Evolution, 23:2214-2219. http://mbe.oxfordjournals.org/cgi/reprint/23/11/2214 citation("seqinr")

See Also

zscore

Examples

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")