About the Condon Adaptivity Index - (Feb/25/2008 )
CAn anyone show the example to me??
for example:
RNA: AUG - GAC - CAU - AGA - GGA - CAG - UGA
W --- 1.0 0.291 0.004 0.01 1.0 ---
I want to know how to find the W value???
can anyone show the calculation step by step to me?
Thanks
"W" is the codon frequency. Try googling codon frequency, and you should get to a table that has numbers that resemble your set of numbers.
For example, there is only one codon that codes for Met (ATG), so it has a W value of 1.0. The GAC codon makes up 29.1% of the codons for Asp (W value .291) etc.
It is important to note that the codon frequency is different with different organisms. Thus, a gene sequence from a human gene might not be efficiently translated in E. coli, because the E. coli codon usage is different to that of humans. I once had a sample that didn't express well, and it turned out that the Leu codon most commonly used in my gene is actually absent in E. coli.
For example, there is only one codon that codes for Met (ATG), so it has a W value of 1.0. The GAC codon makes up 29.1% of the codons for Asp (W value .291) etc.
It is important to note that the codon frequency is different with different organisms. Thus, a gene sequence from a human gene might not be efficiently translated in E. coli, because the E. coli codon usage is different to that of humans. I once had a sample that didn't express well, and it turned out that the Leu codon most commonly used in my gene is actually absent in E. coli.
Thanks!
But I want to know how u can make the value 0.291 for GAC codon, could u explain in detail, thanks
For example, there is only one codon that codes for Met (ATG), so it has a W value of 1.0. The GAC codon makes up 29.1% of the codons for Asp (W value .291) etc.
It is important to note that the codon frequency is different with different organisms. Thus, a gene sequence from a human gene might not be efficiently translated in E. coli, because the E. coli codon usage is different to that of humans. I once had a sample that didn't express well, and it turned out that the Leu codon most commonly used in my gene is actually absent in E. coli.
Thanks!
But I want to know how u can make the value 0.291 for GAC codon, could u explain in detail, thanks
OK. Here is a small part from this IBM document. It looks at the codon frequency of the two Asp codons in E. coli in a number of highly expressed genes, and then compares those frequencies to that of a second set of genes. The final number is the fraction of the total number of possible codons. The process is repeated for the remaining 19 amino acids.
AmAcid Codon Number /1000 Fraction ..
E. coli Asp GAU 149.00 21.63 0.33
Asp GAC 298.00 43.26 0.67