Standard Ambiguity Codes"

In MLMOI: Estimating Frequencies, Prevalence and Multiplicity of Infection

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SNPs

Nucleotide ambiguity code as defined in DNA Sequence Assembler.

|Symbol | Description | Bases represented | Complement | |---|:--------------|:------------:|:----------:| | A | Adenine | A -- -- -- | V | | C | Cytosine | -- C -- -- | H | | G | Guanine | -- -- G -- | D | | T | Thymine | -- -- -- T | B | | W | Weak | A -- -- T | S | | S | Strong | -- C G -- | W | | M | aMino | A C -- -- | K | | K | Keto | -- -- G T | M | | R | puRine | A -- G -- | Y | | Y | pYrimidine | -- C -- T | R | | B | not A | -- C G T | A | | D | not C | A -- G T | C | | H | not G | A C -- T | G | | V | not T | A C G -- | T | | N | any Nucleotide | A C G T | Z | | Z | Zero | -- -- -- -- | N |

Amino Acids and Codons

The standard ambiguity codes for nucleotides and for the one-letter and three-letter designations of amino acids. Notice that all the entries in the same row encodes to the corresponding amino acid.

|Amino Acid (full)| 3-Let | 1-Let | Codons (triplets) | Compressed (compact) | |:----------------|:------|:-----:|:-----------------------------|:---------------------| |Alanine | Ala | A | GCT, GCC, GCA, GCG | GCN | |Cysteine | Cys | C | TGT, TGC | TGY | |Aspartic | Asp | D | GAT, GAC | GAY | |Glutamic | Glu | E | GAA, GAG | GAR | |Phenylalanine | Phe | F | TTT, TTC | TTY | |Glycine | Gly | G | GGT, GGC, GGA, GGG | GGN | |Histidine | His | H | CAT, CAC | CAY | |Isoleucine | Ile | I | ATT, ATC, ATA | ATH | |Lysine | Lys | K | AAA, AAG | AAR | |Leucine | Leu | L | TTA, TTG, CTT, CTC, CTA, CTG | YTR, CTN | |Methionine | Met | M | ATG | | |Asparagine | Asn | N | AAT, AAC | AAY | |Proline | Pro | P | CCT, CCC, CCA, CCG | CCN |
|Glutamine | Gln | Q | CAA, CAG | CAR | |Arginine | Arg | R | CGT, CGC, CGA, CGG, AGA, AGG | CGN, MGR | |Serine | Ser | S | TCT, TCC, TCA, TCG, AGT, AGC | TCN, AGY | |Threonine | Thr | T | ACT, ACC, ACA, ACG | ACN | |Valine | Val | V | GTT, GTC, GTA, GTG | GTN | |Tryptophan | Trp | W | TGG | | |Tyrosine | Tyr | Y | TAT, TAC | TAY |

MLMOI documentation built on Jan. 11, 2020, 9:22 a.m.