Codon Adaptation Index

Question

[tigeradab]

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?

[5heikki]

emboss ships with algorithms for CAI analysis.

Answer 1

[abdulwrs7]

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.

Click on this link to explore more:Implementation Of Codon Adaptation Index (CAI) Using Biopython

Answer 2

[Charles Warden]

If you happen to be interested in yeast, I downloaded the CAI values from a supplemental table from this paper:

http://mbe.oxfordjournals.org/content/23/2/327.long

with my analysis discussed in this paper:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001559

If you aren't interested in yeast, perhaps the Drummond et al. paper can at least provide some helpful pointers.

Answer 3

[Nitha]

While Running codonW, it automatically generates the reference set ie potential gene. u can use these data for your cal analysis.

More clearly:

It generates files like cai.coa, fop.coa, cbi.coa you can use these file for corresponding analysis.

for your questions, you can use cai.coa file as the reference set for CAI calculations.

Answer 4

[anamaria]

For those interested in calculating codon usage statistic, including CAI, there's our R/Bioconductor package that lets you do this, and it comes with some nice visualisations, too https://bioconductor.org/packages/release/bioc/html/coRdon.html

[h.mon]

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.

[anamaria]

Cool, will do, thank you