CAIcal: a combined set of tools to assess codon usage adaptation

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• The Codon Adaptation Index (CAI) measures synonymous codon usage bias in DNA/RNA sequences.
• CAI quantifies the similarity between a gene's codon usage and a reference set's codon frequency.

Purpose of the Study:

• To introduce CAIcal, a comprehensive web server for calculating and analyzing the Codon Adaptation Index (CAI).
• To provide a user-friendly platform for assessing codon usage adaptation in biological sequences.

Main Methods:

• Developed CAIcal as a web server and standalone application.
• Implemented utilities for calculating CAI on individual sequences or multiple sequence alignments.
• Included automated calculation of CAI and its expected value.

Main Results:

• CAIcal offers a complete suite of tools for CAI analysis.
• The server provides graphical representations of CAI values.
• Automated CAI calculation and expected value determination are available.

Conclusions:

• CAIcal serves as a valuable resource for codon usage adaptation studies.
• The tool assists in genome annotation by analyzing codon bias.