Question: Codon Adaptation Index (Cai)
2
gravatar for martin.kavscek
6.3 years ago by
martin.kavscek20 wrote:

I am relativly new to the field and I am dealing now with the codon usage for different proteins in several pathways to see if there is corelation. Just to be sure about the metod - As I would like to compare two different organism I would like to set the reference codon usage table of the whole genome, and then calculate CAI for each gene in each organism. Will I be than able to relevantly compare CAI from homologous genes?

Thank you very much for your answers! Martin Kavšček

• 8.2k views
ADD COMMENTlink modified 5.1 years ago by bioee0 • written 6.3 years ago by martin.kavscek20

Look at these servers for CAI tools:

http://genomes.urv.es/CAIcal/

http://gcua.schoedl.de/sequential_v2.html

http://sysbio.cvm.msstate.edu/CodonO/

http://www.genscript.com/cgi-bin/tools/rare_codon_analysis

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Rm7.9k

You should make sure that the genomes you're testing have a codon bias, not every genome is biased. A simple test is to compare the codon frequencies between highly expressed genes and the rest of the genes in each genome.

ADD REPLYlink written 6.3 years ago by Asaf6.1k
2
gravatar for Anthony Mathelier
6.3 years ago by
University of Oslo, Oslo, Norway
Anthony Mathelier870 wrote:

You should use CAIjava (http://www.ihes.fr/~carbone/materials/description.html) which introduces a correcting factor in the original formula proposed by Sharp and Li (Sharp and Li, 1987), compute the global codon adaptation index, (gCAI) and determine a set S of coding sequences with high gCAI values. Ultimately, CAI values can be computed on codon weights calculated on S.

Hence it refines the computation of CAI without using the starting set of highly expressed genes only to compute the codon biais. This method has been used successfully in many other papers.

http://www.ihes.fr/~carbone/papers/Bioinformatics.pdf .

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Anthony Mathelier870

Thank you very much for that. I will look into it. What I do not want is to use a reference set S that is based on some highly expressed genes, because I would like to compare the CAI of enzymes in glycolysis for 2 different organism.

ADD REPLYlink written 6.3 years ago by martin.kavscek20

Then you should definitely use this tool which computes the set S of interest directly from the genome.

ADD REPLYlink written 6.3 years ago by Anthony Mathelier870
0
gravatar for martin.kavscek
6.3 years ago by
martin.kavscek20 wrote:

I have additional question - if I will compute gCAI with this script the set reference (S) would again use genes that have high frequencies of highly used codons. What I would like to do is to have a set of genes that have average codon usage as a reference (and therefore average exspression) or to use a whole genome as a set of reference. In that way I would be able to compare expression values of homologous proteins in two different organism.

Am I thinking in the right direction or not ? :)

Thank you for your answers. Martin

ADD COMMENTlink written 6.3 years ago by martin.kavscek20
2

Add as new Question...

ADD REPLYlink written 6.3 years ago by Rm7.9k
0
gravatar for bioee
5.1 years ago by
bioee0
United States
bioee0 wrote:

For calculating CAI or RSCU mentioned in Sharp and Li (Sharp and Li, 1987), you can use the open source biopython, it is so easy to use. 

Also, you should check another online tool http://www.biologicscorp.com/tools/CAICalculator which use a genomic codon usage or reference sequence for calculating. 

ADD COMMENTlink written 5.1 years ago by bioee0
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