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