What are the base degeneracy codes that you use (e.g., R, W, K, V, S)?
The one letter codes for degenerate bases are determined by the International Union of Biochemistry (IUB), according to the bases' properties.
For example, the letter Y is the symbol for an unspecified pyrimidine nucleoside and the letter R is for an unspecified purine nucleoside.
The letters used for ordering degenerate bases are as follows:
Be sure to use upper case letters (e.g., R, N, S) to denote mixed (degenerate, random, wobble) bases. Lower case letters are not recognized as they are used to denote certain modifications and RNA bases.
Want more information? Explore IDT's Mixed bases product page