Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.
Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.
draw.rearranged.oriloc(rearr.ori, breaks.gcfw = NA, breaks.gcrev = NA, breaks.atfw = NA, breaks.atrev = NA)
rearr.ori |
A data frame obtained with the |
breaks.gcfw |
The coordinates of the breakpoints in the GC-skew,
for forward transcribed protein coding sequences. These coordinates
can be obtained with the |
breaks.gcrev |
The coordinates of the breakpoints in the GC-skew,
for reverse transcribed protein coding sequences. These coordinates
can be obtained with the |
breaks.atfw |
The coordinates of the breakpoints in the AT-skew,
for forward transcribed protein coding sequences. These coordinates
can be obtained with the |
breaks.atrev |
The coordinates of the breakpoints in the AT-skew,
for reverse transcribed protein coding sequences. These coordinates
can be obtained with the |
J.R. Lobry, A. Necşulea
Necşulea, A. and Lobry, J.R. (2007) A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry. Molecular Biology and Evolution, 24:2169-2179.
## Not run:
### Example for Chlamydia trachomatis ####
### Rearrange the chromosome and compute the nucleotide skews ###
#r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr"),
# g2.coord = system.file("sequences/ct.coord", package = "seqinr"))
r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr"),
g2.coord = system.file("sequences/ct.coord", package = "seqinr"))
### Extract the breakpoints for the rearranged nucleotide skews ###
breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"),
nbreaks = c(2, 2), gridsize = 50, it.max = 100)
### Draw the rearranged nucleotide skews and ###
### place the position of the breakpoints on the graphics ###
draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks,
breaks.gcrev = breaks$gcrev$breaks)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.