cai2 1.0.5

cai2 - Codon Adaptation Index

An implementation of Sharp and Li's 1987 formulation

of the codon adaption index.

This is an update of cai providing the same functionality, but now works with all python 3 versions. This version also has more tests, some derived from the Sharp and Li 1987 paper above.

This module can be installed with the following command:

$ pip install cai2

Use:

Finding the CAI of a sequence is easy:

from cai2 import CAI
CAI("ATG...", reference=["ATGTTT...", "ATGCGC...",...])
0.24948128951724224

Determining which sequences to use as the reference set is left to the user, though the HEG-DB is a great resource of highly expressed genes.

Citation

Lee, B. D. (2018). Python Implementation of Codon Adaptation Index.

Journal of Open Source Software, 3 (30), 905.

https://doi.org/10.21105/joss.00905

:

@article{Lee2018,

doi = {10.21105/joss.00905},

url = {https://doi.org/10.21105/joss.00905},

year = {2018},

month = {oct},

publisher = {The Open Journal},

volume = {3},

number = {30},

pages = {905},

author = {Benjamin D. Lee},

title = {Python Implementation of Codon Adaptation Index},

journal = {Journal of Open Source Software}

The original creator was benjamin_lee@college.harvard.edu. This version was created by Björn Johansson as it is needed for optional functionality for pydna.

Reference

Sharp, P. M., & Li, W. H. (1987). The codon adaptation index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 15(3), 1281–1295.