codon

On top of that, some codons have a special meaning, such as "\\n".

The article said its a mutation, but maybe those with the mutation exhibit a certain codon pair.

Those special codons are called "stop codon", because it marks the end of a protein and the program stops decoding from this point on.

Is codon usage between host and parasite similar?

"over the last few years it's also been clear that codon bias can be evolutionarily constrained.

You'll see hand-wavy explanations for differences in codon usage in really old textbooks.

I've always assumed it was some sort of metabolic constraint, as in more efficient production of certain tRNAs putting a constraint on codon usage.

"This is a much older question than the last few years -- it's one of those "evergreen" questions that's been around for almost as long as we've been able to do statistics on codon prevalence.

Actually I didn't know exonic TF binding was even significant enough to put synonymous codon variation under constraint.

This is very similar to earlier discoveries that the choice of codon can be intimately tied in with protein domains folding; allowing proteins to partially fold while the remainder is "stalled" on the ribosome waiting for the rare codon.