Quick question about expected codon frequencies

Question

[schlogl]

Hi There

I read some papers on the issue, but I got a doubt about the frequency calculation due a difference in using 64 codons and 61 (excluding the 3 stops)?

codon[aac] = num codons aac / num codons in the table codon

Do you have a suggestion to use? 64 or 61.

Thank you.

PS- Sorry to bother with this kind of question but I don't have any friend that knows the subject to discuss this silly doubts.

[schlogl]

None? 8( ...........

Answer 1

[Asaf]

It all depends on why you want to calculate it. Usually the research related to codon frequency is related to tRNA so there is no reason to include the stop codons.

[psschlogl]

Thank you for your time Asaf

[LauferVA]

as a parenthetical note, you will get the best responses here if you state YOUR case as clearly as you can.

Now, in this case, Asaf accounted for that, but in other cases you might get a single link, or the most common answer, with no clarification.

If your experimental case just so happens to be different than the most common case, theres a chance you take an approach thats worse for you.

But, this cant (or is very unlikely) to happen if you provide context - so provide context :-)