I'm looking to generate data based on the DNA composition of a region of my genomes (data is incomplete genomes from HiSeq runs in fasta format). I'm looking for software which will give me sliding windows for GC content, GC skew, codon bias etc. I would like to use something which I can use with or plug into R.
1 Answer
There are more R packages available that calculate GC content, for example Ape's GC.content()
function.
For example:
> library(ape)
> data(woodmouse)
> GC.content(woodmouse)
[1] 0.3873347
With a sliding window is in Biostrings
package.
> library(Biostrings)
> DNA <- DNAString("ACTGAAACCGTGGCAGTTTGAC")
> letterFrequencyInSlidingView(DNA, view.width=4,letters="CG")
For codon usage bias, I think cubfits
or sscu
packages might be useful.
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$\begingroup$ According to ape gc.content will only give a percentage. I'm looking for the overall distribution. $\endgroup$– AudileFAug 10, 2017 at 10:23
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$\begingroup$ The definition of GC content is a percentage. $\endgroup$– bennAug 10, 2017 at 10:56