CAI 1.0.0

Python implementation of codon adaptation index

An implementation of Sharp and Li’s 1987 formulation of the codon adaption index.

Installation

This module is available from PyPi and can be downloaded with the following command:

$ pip install CAI

To install the latest development version:

$ git clone https://github.com/Benjamin-Lee/CodonAdaptationIndex.git
$ cd CodonAdaptationIndex/
$ pip install -e .

Quickstart

Finding the CAI of a sequence is easy:

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

Similarly, from the command line:

$ CAI -s sequence.fasta -r reference_sequences.fasta
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.

Contributing

Feel free to contribute, open issues, or let me know about bugs. Anything is welcome!

Citation

Benjamin Lee. (2017). Python Implementation of Codon Adaptation Index. Zenodo. http://doi.org/10.5281/zenodo.843854

JOSS citation coming soon.

Contact

I’m available for contact at [e-mail].

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.