rnafolding

rnafolding is a package to predict RNA scructure thermodynamically using sliding windows approach.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("ruthkr/rnafolding")

Quick start

This is a basic example which shows you how to run windowed folding from a FASTA file:

# Load the package
library(rnafolding)

# Define the FASTA path from the sample 5S rRNA sequence
seq_5S <- system.file("extdata", "5S.fasta", package = "rnafolding")

# Fold 5S with Sliding Windows
windows_5S <- rnafolding::fold(
  filename = seq_5S,
  winsize = 50,
  stepsize = 5
)

After getting the windowed folding results, you can plot the structure map as follows:

plot_structure_map(
  windows_5S,
  plot_list = c("entropy", "bpp")
)