Codon Usage Bias (CUB) in Julia

CUBScout calculates Codon Usage Bias (CUB) and related expressivity predictions. Currently, CUBScout calculates:

• Six measures of codon usage bias:
  • B, from Karlin and Mrazek, 1996
  • ENC, from Wright 1990
  • ENC', from Novembre, 2002
  • MCB, from Urrutia and Hurst, 2001
  • MILC, from Supek and Vlahovicek, 2005
  • SCUO, from Wan et al., 2004
• Five expressivity measures based on codon usage bias:
  • CAI, from Sharp and Li, 1987
  • E, from Karlin and Mrazek, 1996
  • FOP, from Ikemura, 1981
  • GCB, from Merkl, 2003
  • MELP, from Supek and Vlahovicek, 2005

CUBScout is based off of the fabulous coRdon package in R by Anamaria Elek, Maja Kuzman, and Kristian Vlahovicek. I am grateful for their clear code and would encourage you to cite coRdon as well when using CUBScout.

You can install CUBScout by:

using Pkg
Pkg.add(url = "https://github.com/gus-pendleton/CUBScout.jl")

CUBScout is under active development, and I welcome contributions or suggestions! Additional features I'm working on/would like to incorporate:

• Performance improvements
• Plotting support (e.g. BPlots)
• Additional CUB measures, including S, RCDI, CDC, RCA, RCSU, and RCBS
• Growth predictions derived from CUB, such as those in growthpred and gRodon