Question: Codon Adaptation Index
0
gravatar for tigeradab
4.8 years ago by
tigeradab40
India
tigeradab40 wrote:

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 index • 1.5k views
ADD COMMENTlink modified 4 days ago by anamaria30 • written 4.8 years ago by tigeradab40

emboss ships with algorithms for CAI analysis.

ADD REPLYlink written 4.8 years ago by 5heikki7.8k
0
gravatar for Charles Warden
4.8 years ago by
Charles Warden5.6k
Duarte, CA
Charles Warden5.6k wrote:

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.

ADD COMMENTlink written 4.8 years ago by Charles Warden5.6k
0
gravatar for Nitha
2.8 years ago by
Nitha10
Nitha10 wrote:

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.

ADD COMMENTlink written 2.8 years ago by Nitha10
0
gravatar for anamaria
4 days ago by
anamaria30
anamaria30 wrote:

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

ADD COMMENTlink written 4 days ago by anamaria30

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.

ADD REPLYlink written 4 days ago by h.mon21k

Cool, will do, thank you

ADD REPLYlink written 4 days ago by anamaria30
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