What are the steps to calculate Codon Adaption Index using codonw? How to give reference set of genes to the codonw software? Other than codonw, is there any other software that computes and gives CAI? Also, is there any software that calculates CAI using Carbone's method?
Codon Adaptation Index (CAI) was first introduced by Sharp and Li to measure synonymous codon usage bias for a DNA or RNA sequence.It also measures the resemblance between the synonymous codon usage of a gene and the synonymous codon frequencies of a reference set.CAI was originally proposed to provide an estimate that can be used across genes and species, ranging from 0 to 1.
If a gene always uses the most frequently used synonymous codon in the reference set,then CAI=1. If a gene always uses the least frequently used synonymous codon in the reference set,then CAI=0.
Hi, your tool will have more visibility - hence it will be more beneficial to both you and your potential users - if you create a new post, choose Tool as post type, and provide a nice description and possibly one or two examples.
emboss ships with algorithms for CAI analysis.