dinucl: Mean zscore on 242 complete bacterial chromosomes

In seqinr: Biological Sequences Retrieval and Analysis

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)

Format

List of two dataframes of 242 chromosomes and 16 dinucleotides: one for intergenic, one for coding sequences.

intergenic

the mean of zscore computed with the base model on each intergenic sequence

coding

the mean of zscore computed with the codon model on each coding sequence

References

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")

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")

seqinr documentation built on May 29, 2024, 6:36 a.m.