Resources
The lookup tables the tools use, written out in full. No sign-in, no download, and nothing behind a link that turns out to be a stub — the two reference tables below are on this page.
IUPAC nucleotide codes
The single-letter codes for defined and ambiguous bases, and what each one complements to. Every BioABC tool recognises all of them.
| Code | Meaning | Matches | Complement |
|---|---|---|---|
| A | Adenine | A | T |
| C | Cytosine | C | G |
| G | Guanine | G | C |
| T | Thymine | T | A |
| U | Uracil (RNA) | U | A |
| R | Purine | A G | Y |
| Y | Pyrimidine | C T | R |
| S | Strong (three H-bonds) | G C | S |
| W | Weak (two H-bonds) | A T | W |
| K | Keto | G T | M |
| M | Amino | A C | K |
| B | Not A | C G T | V |
| D | Not C | A G T | H |
| H | Not G | A C T | D |
| V | Not T | A C G | B |
| N | Any base | A C G T | N |
| - | Gap or deletion | — | - |
Ambiguity codes are counted but excluded from percentage denominators by default, because a code such as N could be any base. Every tool states which convention it used next to its result.
The standard genetic code
All 64 codons, NCBI translation table 1 — the code the translator uses unless you pick another. Read down each column.
TTTFPhe
TTCFPhe
TTALLeu
TTGLLeu
TCTSSer
TCCSSer
TCASSer
TCGSSer
TATYTyr
TACYTyr
TAA—Stop
TAG—Stop
TGTCCys
TGCCCys
TGA—Stop
TGGWTrp
CTTLLeu
CTCLLeu
CTALLeu
CTGLLeu
CCTPPro
CCCPPro
CCAPPro
CCGPPro
CATHHis
CACHHis
CAAQGln
CAGQGln
CGTRArg
CGCRArg
CGARArg
CGGRArg
ATTIIle
ATCIIle
ATAIIle
ATGMMet
ACTTThr
ACCTThr
ACATThr
ACGTThr
AATNAsn
AACNAsn
AAAKLys
AAGKLys
AGTSSer
AGCSSer
AGARArg
AGGRArg
GTTVVal
GTCVVal
GTAVVal
GTGVVal
GCTAAla
GCCAAla
GCAAAla
GCGAAla
GATDAsp
GACDAsp
GAAEGlu
GAGEGlu
GGTGGly
GGCGGly
GGAGGly
GGGGGly
Start codon (ATG)Stop codonWritten 5′ → 3′, DNA bases
Written explanations
Short pieces on the arithmetic behind the tools — why two calculators disagree, and which convention to trust.
- Cornish-Bowden, A. (1985). Nomenclature for incompletely specified bases in nucleic acid sequences. Nucleic Acids Research 13(9), 3021–3030. — the ambiguity codes in the first table.
- NCBI Taxonomy. The Genetic Codes, translation table 1. — the codon assignments in the second table.
- NCBI. FASTA format description, BLAST user documentation. — the header and sequence-line conventions the parsers follow.
- SantaLucia, J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS 95(4), 1460–1465. — the basis for the melting-temperature calculator when it ships.