Nucleic Acid Notation - IUPAC Notation

IUPAC Notation

Degenerate base symbols in biochemistry are an IUPAC representation for a position on a DNA sequence that can have multiple possible alternatives. These should not be confused with non-canonical bases because 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).

Under the commonly used IUPAC system, nucleobases are represented by the first letters of their chemical names: uanine, ytosine, denine, and hymine. This shorthand also includes eleven "ambiguity" characters associated with every possible combination of the four DNA bases. The ambiguity characters were designed to encode positional variations found among families of related genes. The IUPAC notation, including ambiguity characters and suggested mnemonics, is shown in Table 1.

Despite its broad and nearly universal acceptance, the IUPAC system has a number of limitations, which stem from its reliance on the Roman alphabet. The poor legibility of upper-case Roman characters, which are generally used when displaying genetic data, may be chief among these limitations. The value of external projections in distinguishing letters has been well documented. However, these projections are absent from upper case letters, which in some cases are only distinguishable by subtle internal cues. Take for example the upper case C and G used to represent cytosine and guanine. These characters generally comprise half the characters in a genetic sequence but are differentiated by a small internal tick (depending on the typeface). Nevertheless, these Roman characters are available in the ASCII character set most commonly used in textual communications, which reinforces this system's ubiquity.

Another shortcoming of the IUPAC notation arises from the fact that its eleven ambiguity characters have been selected from the remaining characters of the Roman alphabet. The authors of the notation endeavored to select ambiguity characters with logical mnemonics. For example, S is used to represent the possibility of finding cytosine or guanine at genetic loci, both of which form trong cross-strand binging interactions. Conversely, the weaker interactions of thymine and adenine are represented by a W. However, convenient mnemonics are not as readily available for the other ambiguity characters displayed in Table 1. This has made ambiguity characters difficult to use and may account for their limited application.