# CUBScout.jl: Codon Usage Bias in Julia

**URL:** https://discourse.julialang.org/t/cubscout-jl-codon-usage-bias-in-julia/99774
**Category:** Package Announcements
**Tags:** biology
**Created:** [June 2, 2023, 3:04pm UTC](https://discourse.julialang.org/t/cubscout-jl-codon-usage-bias-in-julia/99774 "2023-06-02T15:04:05Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![gus-pendleton](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/gus-pendleton/32/49241_2.png) [@gus-pendleton](https://discourse.julialang.org/u/gus-pendleton)
#### Post date: [June 2, 2023, 3:04pm UTC](https://discourse.julialang.org/t/cubscout-jl-codon-usage-bias-in-julia/99774/1 "2023-06-02T15:04:05Z")

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[CUBScout](https://github.com/gus-pendleton/CUBScout.jl) 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](https://www.bioconductor.org/packages/release/bioc/html/coRdon.html) 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