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. . pmid:2657727.
- Irwin B, Heck JD, and Hatfield GW. . pmid:7559409.
- Trinh R, Gurbaxani B, Morrison SL, and Seyfzadeh M. . pmid:14644097.