---
title: "Standard Ambiguity Codes"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Standard Ambiguity Codes}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---


```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## 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                  |



