IUPAC expander
Every sequence a degenerate primer stands for, and the count. Or the other way round.
Every sequence a degenerate primer stands for, and the count. Or the other way round.
A single letter that stands for more than one base. They were agreed by the IUPAC and IUB nomenclature commission so that a position which is uncertain, variable between species, or deliberately mixed during oligonucleotide synthesis can be written in one character. R is A or G, N is any base, and so on. Degenerate primers, consensus motifs and restriction site definitions are all written this way.
| Code | Bases | Meaning | Degeneracy | Complement |
|---|---|---|---|---|
| A | A | Adenine | 1 | T |
| C | C | Cytosine | 1 | G |
| G | G | Guanine | 1 | C |
| T | T | Thymine (U in RNA) | 1 | A |
| R | A G | Purine | 2 | Y |
| Y | C T | Pyrimidine | 2 | R |
| S | C G | Strong, three hydrogen bonds | 2 | S |
| W | A T | Weak, two hydrogen bonds | 2 | W |
| K | G T | Keto | 2 | M |
| M | A C | Amino | 2 | K |
| B | C G T | Not A | 3 | V |
| D | A G T | Not C | 3 | H |
| H | A C T | Not G | 3 | D |
| V | A C G | Not T | 3 | B |
| N | A C G T | Any base | 4 | N |
Each position is independent, so the number of concrete sequences is the product of the degeneracies:
Worked example. The universal 16S primer 515F is GTGYCAGCMGCCGCGGTAA, 19 nt with one Y and one M. Its degeneracy is 2 × 2 = 4, so the tube holds four oligonucleotides:
The count is kept as an exact integer, so a sequence of 200 N is reported as 2.58 × 10120 combinations rather than overflowing to infinity. Only the list of sequences is limited.
The second tab does the reverse. Give it aligned sequences of the same length, one per line or as FASTA, and every column is replaced by the code for the set of bases in it: a column with only A and G becomes R, a column with C, G and T becomes B. Feed the four sequences above back in and you get GTGYCAGCMGCCGCGGTAA again. Because the codes describe columns independently, a consensus can cover more sequences than you supplied; the tool reports how many, so you can tell an exact collapse from a loose one.
To flip a degenerate sequence to the other strand, use thereverse complement tool, which keeps IUPAC codes. To check a primer pair for self-annealing, use the primer dimer checker.
Multiply the degeneracy of every position: 1 for A, C, G and T, 2 for R, Y, S, W, K and M, 3 for B, D, H and V, and 4 for N. The primer GTGYCAGCMGCCGCGGTAA has one Y and one M, so it is a mixture of 2 × 2 = 4 sequences.
Degeneracy grows exponentially. Twelve N positions already give 16.7 million sequences, more than a browser can list. The count is always exact, and the list is cut at the limit you choose, 100, 1,000 or 10,000.
Yes. A sequence that contains U and no T is treated as RNA and the expanded sequences are written with U. IUPAC codes mean the same bases in both alphabets.
It reads a set of aligned sequences of the same length and writes one sequence in which every column is replaced by the IUPAC code for the bases seen in that column. It is the inverse of expanding, and it is how a degenerate primer is designed from an alignment.
IUPAC codes describe each position on its own, so they cannot record which bases go together. Two sequences ACG and TCT collapse to WCK, which also covers ACT and TCG. The tool reports how many sequences the consensus covers so you can see the difference.