CUBScout

Codon Usage Bias (CUB) in Julia

CUBScout helps you work with codons! Beyond counting codons and finding codon frequency, 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 CUBScout

Or for the dev version:

pkg> add CUBScout#main

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