Forum: Correspondance Analysis by using CodonW- codon usage biase
gravatar for Nitha
3.0 years ago by
Nitha10 wrote:

Hi All, 

How to create reference set of highly expressed genes for CAI. default its E.coli, My genome is Chlamydia trachomatis so i have to create reference set for performing some analysis Fop, CAI, CBI etc.

can anyone guide me how to create the highly expressed reference set and to give put these file.

They have asked to select menu 3-- ie "change defaults settings" but i am not able to change..

and need help to interpret the values and make meaning full charts.

I am using offline codonW 1.4, in windows platform 


ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Nitha10

Hi Nitha, I am struggling with the same problem now. Even though you mentioned that after performing COA, you got the file containing highly expressed genes, I could not understand exactly how to do so. Can you please explain the steps in detail to perform COA so that I can get the reference set of highly expressed genes. I would be very much thankful to you for your help.


ADD REPLYlink written 24 months ago by minaljamsandekar0

Hi Minal,

Can you make it more clear about your needs.

  1. so far what you have done, had you calculated the codon indices?
  2. What exactly your looking for ? HEG or to do COA?

If you give me an out line about your problem definitely I can help you.


ADD REPLYlink modified 24 months ago • written 24 months ago by Nitha10

Please make it clear, so i can help you

ADD REPLYlink modified 24 months ago • written 24 months ago by Nitha10

Thanks a lot Nitha. Yeah, I have calculated ENc, G+C, GC3s, L_Syn, L_aa, Gravy and Aromo. Now for estimating other indices, I need a reference set of highly expressed genes, and for that I need to change the default values of CAI/Fop/CBI. In your earlier comment, you mentioned that by doing COA, we can get a reference set. So I want to know - exactly where to look for getting a reference set? I carried out COA analysis and got 11 output files. So now I am confused and not understanding how to interpret such output files and how to get reference set out of it? Is my question clear now?

Thank you, Minal

ADD REPLYlink written 23 months ago by minaljamsandekar0

Hi Minal,

Thanks for making me clear.

one more clarification, in what platform your working windows are Linux?

1) Reference set for 8 different species are identified and their are values are kept default in codonW. In my case, my organism was gram negative bacteria so I opted E.coli and performed for further calculation. So, you can choose according to your organism. (Read John Peden thesis - codonW)

2) After this settings, go for 5-COA and once you complete, as you said you get 11 files. In that cai.coa, fop.coa, cbi.coa these are the files which gives the values used for calculating CAI, CBI and Fop. use this. (cai.coa, cbi.coa, fop.coa- check these files they have given values)

when it ask whether to use personal choice, choose-yes-and give this file name cai.coa etc. (Read CodonW - SourceForge they have mentioned it clearly).

And another thing in codon usage analysis you can create your own reference set for your organism (please refer sharp paper and ikemura on codon usage analysis).

if you have further doubts in calculation please do ask.

ADD REPLYlink modified 23 months ago • written 23 months ago by Nitha10

Hi Nitha,

Thank you so much for explaining each and every detail. It helped me a lot. I carried out COA and understanding the output files too. I thoroughly read the Thesis by John Peden. It is so much helpful. I have installed CodonW on both Windows as well as on Linux. And I am using both the OS. I am working on vertebrate species. So, I have to input the personal choice for calculating CAI, Fop and CBI indices. While doing so, I came across one more problem. You said that when the program will ask for personal choice, I have to provide cai.coa file. However, the program does not ask for the input file where I can type cai.coa. After selecting menu 1, it shows following lines on screen:

"The reference set currently selected is that of E.coli. See the menu 'change defaults' to change this selection If you wish to use a personal choice of CAI values please continue and you will be prompted for input Press return or enter to continue"

And when I press enter, it shows all the options under codon usage indices menu. But it does not show the option to choose yes for the personal choice.

Can you please suggest me how do I go ahead with this? Do I send you my cai.coa file to get more clear idea and by using which you can also look for what is happening exactly?

Thank a lot for your time and help. Minal

ADD REPLYlink written 23 months ago by minaljamsandekar0


Apologies for delay. Can I know which version of Codon W you are using (Because when i was working in windows it ask the personal choice). Please send me your mail ID so that I can send you all the details with pictures which explains the steps. Because here I am unable to attach all the details.

ADD REPLYlink written 23 months ago by Nitha10

Hi Nitha, I am sorry for replying so late. I got engaged with other things and now I again started with CodonW. I have version 1.4.4 which is latest and is completely same as v1.4.2, so I don't think different versions cause any issue. My email id is Can you please email the detailed steps?

Awaiting your response, Thank you so much, Minal

ADD REPLYlink written 20 months ago by minaljamsandekar0
gravatar for Nari
3.0 years ago by
United States
Nari870 wrote:

For calculating CAI for your organism, they are using highly expressed genes from Three organisms E.coli, B. subtilis or Saccharomyces cerevisiae and no other option in CodonW. 

After Option 3 : enter option 6 or 7 for Fop/CBI or CAI respectively. 

after 6 or 7 you can select 0, 1 or 2 for any of these 3 organisms. press Enter till the main menu arises.

then GO TO option 4 "Codon Usage indices" 

then enter 12 for calculating listed parameters.

Enter come back to main menu then run by entering "R". the filename.out in that folder will give you all parameters.

ADD COMMENTlink written 3.0 years ago by Nari870

Hi  Mr.Naren,

Thank you for your reply! I have found out the answer for question.. When i have performed COA, for my species it automatically, produced the file contain highly expressed gene details for my species, using this i performed codon indices like, CAI, Fop,CBI.  If, I am not wrong.. I observed that CodonW its automatically gives the reference set of expressed gene for their corresponding species. Using this we can change the default to our interest.

Thank you for your time to give solution for my questions..



ADD REPLYlink written 3.0 years ago by Nitha10

Hello @Nitha, if you got the answer then accept the answer.

ADD REPLYlink written 2.4 years ago by Nari870
gravatar for Nitha
3.0 years ago by
Nitha10 wrote:

 Hi All, 

can anyone suggest me a recent research paper which tells "complete steps to follow" while doing Correspondence analysis in Gram-negative bacteria.. .




ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Nitha10
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