Ambiguity codes

Sometimes it is necessary that a certain position in a primer is made ambiguous. This means that the primer is actually a mix of primers, each having one of the nucleotides defined by the ambiguity at that position. For instance, if an ´R´ is encountered in the primer sequence, this means that roughly half of the primers in the mix will have an ´A´ at that position, and the other half a ´G´. The ambiguity codes used in the database have been defined by the Nomenclature Committee of the International Union of Biochemistry, and the following symbols are used:

ambiguity code      nucleotides             meaning
--------------      -----------             -------
     R              A or G                  aRginine
     Y              C or T                  pYrimidine
     S              C or G                  Strong interaction
     W              A or T                  Weak interaction
     K              G or T                  Keto
     M              A or C                  aMino
     B              C or G or T             no A (B follows A in alphabet)
     D              A or G or T             no C (D follows C in alphabet)
     H              A or C or T             no G (H follows G in alphabet)
     V              A or C or G             no T (H follows T and U in alphabet)
     N              A or C or G or T        aNy

Document last updated: Tue Jul 15 12:00:40 MEST 2003