Relative codon adaptation index, a sensitive measure of codon usage bias

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Synonymous codon usage bias influences gene expression.
• The Codon Adaptation Index (CAI) is a common measure, but has limitations in distinguishing bias levels.
• Existing measures like effective number of codons and SCUMBLE offsets have varying correlations with biological factors.

Purpose of the Study:

• To develop a more sensitive and accurate measure of synonymous codon usage bias.
• To introduce the Relative Codon Adaptation Index (rCAI) as an improvement over CAI.
• To evaluate rCAI's performance against existing methods and biological correlates.

Main Methods:

• Calculated rCAI by subtracting background codon usage (from noncoding frames) from coding frame codon usage.
• Compared rCAI's performance with CAI and other bias measures.
• Assessed correlations between rCAI and translation efficiency/protein abundance.

Main Results:

• rCAI demonstrates a higher signal-to-noise ratio than CAI for discriminating codon bias.
• rCAI shows comparable or better correlation with translation efficiency and protein abundance than CAI.
• Identified dominant coding frames in overlapping regions using rCAI.

Conclusions:

• rCAI is a simple, sensitive, and potentially superior measure for synonymous codon usage bias.
• rCAI can effectively differentiate between highly biased and unbiased genomic regions.
• rCAI may serve as a valuable substitute for CAI in various bioinformatics applications.