Degenerate bases

Degenerate base symbols in biochemistry are a IUPAC representation for a position on a sequence that can be have multiple possible alternatives. These should not be confused with non-canonical bases, each particular sequence will have in fact one of the regular bases. These are used to encode the consensus sequence of a population of aligned sequences and are used for example in phylogenetic analysis to summarise into one multiple sequences or for BLAST searches, even though IUPAC degenerate symbols are masked (as they are not coded).

• A adenosine (A)
• C cytidine (C)
• G guanine (G)
• T thymidine (T)
• U uridine (U)
• W weak (A or T)
• S strong (G or C)
• M amino (A or C)
• K keto (G or T)
• R purine (G or A)
• Y pyrimidine (T or C)
• B not A (G or T or C)
• D not C (G or A or T)
• H not G (A or C or T)
• V not T (G or C or A)
• N any base (A or G or C or T, but not a gap)