FastaUtils: Utilities for DNA/RNA sequence processing

The package FastaUtils provides tools for the manipulation of DNA/RNA sequence data with R. This package is still work in progress.

FastaUtils depends on Biostrings package which can be installed from Bioconductor (see below).

Content

The current version contains the following functions:

• subset.fasta() Select a subset of sequences from a fasta file
• DNA2RNA() Convert a DNA fasta to an RNA fasta
• RNA2DNA() Convert a RNA fasta to an DNA fasta
• fasta.sample() Select a random sample of sequences
• fasta.cutter() Cuts peaces of a fixed length and a random position for all sequences or for a random sample of sequences

Authors

Guillem Salazar

Citation

To see the preferable citation of the package, type:

citation("FastalUtils")

Software Versions

R: version 3.2.1
RStudio: Version 0.99.467

Contact Info

Guillem Salazar (guillems at ethz.ch)

Installation of the package

• Install the latest version of Biostring from Bioconductor:

source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")

• Install FastaUtils' current development version from Github:

devtools::install_github("GuillemSalazar/FastaUtils")

• After attaching the package, you are ready to start:

library(FastaUtils)