Reckoning / Code of life / The IUPAC letters
Code of life · shorthand
The IUPAC letters
Sequencers are not always sure which base they read, and many enzymes recognise a family of sequences rather than one. The IUPAC–IUB code gives every set of bases its own letter: R for “A or G”, N for “any”. Fifteen letters cover all fifteen non-empty sets of four bases.
Decoder
Find a pattern in a sequence (both strands)
The table
| Letter | Means | Why that letter | Set | Complement |
|---|---|---|---|---|
| A | adenine | Adenine | {A} | T |
| C | cytosine | Cytosine | {C} | G |
| G | guanine | Guanine | {G} | C |
| T | thymine (U, uracil, in RNA) | Thymine | {T} | A |
| R | A or G | puRine | {A, G} | Y |
| Y | C or T | pYrimidine | {C, T} | R |
| S | G or C | Strong: three hydrogen bonds | {C, G} | S |
| W | A or T | Weak: two hydrogen bonds | {A, T} | W |
| K | G or T | Keto | {G, T} | M |
| M | A or C | aMino | {A, C} | K |
| B | C, G or T | not A: B comes after A | {C, G, T} | V |
| D | A, G or T | not C: D comes after C | {A, G, T} | H |
| H | A, C or T | not G: H comes after G | {A, C, T} | D |
| V | A, C or G | not T (not U): V comes after U | {A, C, G} | B |
| N | any base | aNy | {A, C, G, T} | N |
Code: NC-IUB 1985. The sets live in one table in the site’s code; the meanings, the complements and the decoder are all generated from it, and the build checks that the complement of every letter’s complement is the letter itself, and that the meanings above say the same as the sets.
Complementing a set swaps A with T and G with C inside it. Purines become pyrimidines, so R ↔ Y. Strong stays strong and weak stays weak, so S and W are their own complements. Keto and amino swap (K ↔ M), and “not A” becomes “not T” (B ↔ V), just as D ↔ H.