Thanks Artur. Actually, Jcat is a webtool for codon optimization and my microorganism is a yeast but this Jcat has only Saccharomyces cerevisiae codon optimization provision, not for other yeasts. Are there any other tools for codon optimization?

Let me be sure I understand your question. You work on a yeast that isn't S. cerevisiae, S. pombe, or P. pastoris. You want to express a gene from some organism IN YOUR YEAST. In that case, assuming there is no convenient codon usage table for your yeast available, you might look at a few (hopefully) sequenced well-known, well-behaved genes and look at which codons are used, and whether they differ from the organism you wish to express your gene in. I'm asking because I'm thinking this is not what you want to do. (and, if this is what you want to do, the first thing you might try is to just clone the gene and try to express it without optimization...why not...).

If you want to express a gene from your yeast in a well-characterized organism (E. coli, S. cerevisiae), the codon optimization tools will work, because we know a lot about what common model organisms like in terms of codon bias. This is the more likely thing to do (express your gene in E. coli), and, if so, it shouldn't matter that your yeast isn't well studied.

Does that make sense? Hopefully it helps. 

Thanks Lori. I got my answer.

Artur, my yeast is A (source of gene) and B is S. cerevisiae.