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

-peggybee1-

"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.

-swanny-

QUOTE (swanny @ Feb 25 2008, 06:44 PM)
"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.

Thanks!
But I want to know how u can make the value 0.291 for GAC codon, could u explain in detail, thanks

-peggybee1-

QUOTE (peggybee1 @ Feb 26 2008, 05:17 PM)
QUOTE (swanny @ Feb 25 2008, 06:44 PM)
"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.

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

-swanny-