draw.rearranged.oriloc: Graphical representation for rearranged nucleotide skews in...

In seqinr: Biological Sequences Retrieval and Analysis

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

Description

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

Usage

draw.rearranged.oriloc(rearr.ori, breaks.gcfw = NA,
 breaks.gcrev = NA, breaks.atfw = NA, breaks.atrev = NA)

Arguments

rearr.ori	A data frame obtained with the rearranged.oriloc function.
breaks.gcfw	The coordinates of the breakpoints in the GC-skew, for forward transcribed protein coding sequences. These coordinates can be obtained with the extract.breakpoints function.
breaks.gcrev	The coordinates of the breakpoints in the GC-skew, for reverse transcribed protein coding sequences. These coordinates can be obtained with the extract.breakpoints function.
breaks.atfw	The coordinates of the breakpoints in the AT-skew, for forward transcribed protein coding sequences. These coordinates can be obtained with the extract.breakpoints function.
breaks.atrev	The coordinates of the breakpoints in the AT-skew, for reverse transcribed protein coding sequences. These coordinates can be obtained with the extract.breakpoints function.

Author(s)

J.R. Lobry, A. Necşulea

References

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.

See Also

rearranged.oriloc, extract.breakpoints

Examples

## 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)

seqinr documentation built on March 31, 2023, 3:05 p.m.