CAI

Introduction

The efficiency of translating mRNA to protein depends partially on the coding strategy of an mRNA. It is reflected in codon usage bias, which is often measured by codon-specific and gene-specific indices. A representative of the first class is the relatively synonymous codon usage or RSCU (Sharp et al. 1986). A representative of the second class is the codon adaptation index, or CAI (Sharp and Li, 1987).

How to calculate?

Old CAI

\[w_{i j}=\frac{f_{i j . r e f}}{\operatorname{Maxf}_{i, v e f}}\] \[CAI=\exp \left(\frac{\sum_{i=1}^{m} \sum_{j=1}^{n_{i}}\left[f_{i j} \ln \left(w_{i j}\right)\right]}{\sum_{i=1}^{m} \sum_{j=1}^{n_{i}} f_{i j}}\right)\]

New CAI

\[CAI2= \frac{\sum_{i=1}^{m} \sum_{j=1}^{n_{i}}\left[f_{i j} w_{i j}\right]}{\sum_{i=1}^{m} \sum_{j=1}^{n_{i}} f_{i j}}\]

Meaning of value

CAI refers to the adaptation coefficient of all codons encoding the protein for a certain generative if the gene uses the optimal codon. The CAI value is within the range of 0–1. A more considerable value indicates more robust adaptability. CAI value is widely used in the evaluation of gene expression levels.

Sharp et al. 1986

Sharp and Li, 1987

An Improved Implementation of Codon Adaptation Index

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