CUBScout.jl: Codon Usage Bias in Julia

CUBScout is a new package to calculate Codon Usage Bias in Julia. 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.

CUBScout is under active development, and I welcome contributions or suggestions before pushing a stable release to the registry! 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