Apparently there is nonrandom codon pair utilization in many species. Codon pairs may affect translational elongation rates and therefore protein production. (There can be translational pause sites that are species-specific.)
CODA genomics checks and optimizes for such things.
(Note: I haven't read the papers to evaluate this claim. Just posting the info here so that I remember it.)
- Gutman GA and Hatfield GW. Nonrandom utilization of codon pairs in Escherichia coli. Proc Natl Acad Sci U S A. 1989 May;86(10):3699-703.
- Irwin B, Heck JD, and Hatfield GW. Codon pair utilization biases influence translational elongation step times. J Biol Chem. 1995 Sep 29;270(39):22801-6.
- Trinh R, Gurbaxani B, Morrison SL, and Seyfzadeh M. Optimization of codon pair use within the (GGGGS)3 linker sequence results in enhanced protein expression. Mol Immunol. 2004 Jan;40(10):717-22.