GENETIC_CODE: The Standard Genetic Code and its known variants
In anandhupresannan/biostrings: Efficient manipulation of biological strings

Description Usage Arguments Details Value Author(s) References See Also Examples

Two predefined objects (GENETIC_CODE and RNA_GENETIC_CODE) that represent The Standard Genetic Code.

Other genetic codes are stored in predefined table GENETIC_CODE_TABLE from which they can conveniently be extracted with getGeneticCode.

## The Standard Genetic Code:
GENETIC_CODE
RNA_GENETIC_CODE

## All the known genetic codes:
GENETIC_CODE_TABLE
getGeneticCode(id_or_name2="1", full.search=FALSE, as.data.frame=FALSE)

`id_or_name2`	A single string that uniquely identifies the genetic code to extract. Should be one of the values in the `id` or `name2` columns of `GENETIC_CODE_TABLE`.
`full.search`	By default, only the `id` and `name2` columns of `GENETIC_CODE_TABLE` are searched for an exact match with `id_or_name2`. If `full.search` is TRUE, then the search is extended to the `name` column of `GENETIC_CODE_TABLE` and `id_or_name2` only needs to be a substring of one of the names in that column (also case is ignored).
`as.data.frame`	Should the genetic code be returned as a data frame instead of a named character vector?

Formally, a genetic code is a mapping between the 64 tri-nucleotide sequences (called codons) and amino acids.

The Standard Genetic Code (a.k.a. The Canonical Genetic Code, or simply The Genetic Code) is the particular mapping that encodes the vast majority of genes in nature.

GENETIC_CODE and RNA_GENETIC_CODE are predefined named character vectors that represent this mapping.

All the known genetic codes are summarized in GENETIC_CODE_TABLE, which is a predefined data frame with one row per known genetic code. Use getGeneticCode to extract one genetic code at a time from this object.

GENETIC_CODE and RNA_GENETIC_CODE are both named character vectors of length 64 (the number of all possible tri-nucleotide sequences) where each element is a single letter representing either an amino acid or the stop codon "*" (aka termination codon).

The names of the GENETIC_CODE vector are the DNA codons i.e. the tri-nucleotide sequences (directed 5' to 3') that are assumed to belong to the "coding DNA strand" (aka "sense DNA strand" or "non-template DNA strand") of the gene.

The names of the RNA_GENETIC_CODE are the RNA codons i.e. the tri-nucleotide sequences (directed 5' to 3') that are assumed to belong to the mRNA of the gene.

Note that the values in the GENETIC_CODE and RNA_GENETIC_CODE vectors are the same, only their names are different. The names of the latter are those of the former where all occurrences of T (thymine) have been replaced by U (uracil).

Finally, both vectors have an alt_init_codons attribute on them, that lists the alternative initiation codons. Note that codons that always translate to M (Methionine) (e.g. ATG in GENETIC_CODE or AUG in RNA_GENETIC_CODE) are omitted from the alt_init_codons attribute.

GENETIC_CODE_TABLE is a data frame that contains all the known genetic codes listed at ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt. The data frame has one row per known genetic code and the 5 following columns:

name: The long and very descriptive name of the genetic code.
name2: The short name of the genetic code (not all genetic codes have one).
id: The id of the genetic code.
AAs: A 64-character string representing the genetic code itself in a compact form (i.e. one letter per codon, the codons are assumed to be ordered like in GENETIC_CODE).
Starts: A 64-character string indicating the Initiation Codons.

By default (i.e. when as.data.frame is set to FALSE), getGeneticCode returns a named character vector of length 64 similar to GENETIC_CODE i.e. it contains 1-letter strings from the Amino Acid alphabet (see ?AA_ALPHABET) and its names are identical to names(GENETIC_CODE). In addition it has an attribute on it, the alt_init_codons attribute, that lists the alternative initiation codons. Note that codons that always translate to M (Methionine) (e.g. ATG) are omitted from the alt_init_codons attribute.

When as.data.frame is set to TRUE, getGeneticCode returns a data frame with 64 rows (one per codon), rownames (3-letter strings representing the codons), and the 2 following columns:

AA: A 1-letter string from the Amino Acid alphabet (see ?AA_ALPHABET) representing the amino acid mapped to the codon ("*" is used to mark the stop codon).
Start: A 1-letter string indicating an alternative mapping for the codon i.e. what amino acid the codon is mapped to when it's the first tranlated codon.

The rownames of the data frame are identical to names(GENETIC_CODE).

H. Pagès

All the known genetic codes are described here:

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

The "official names" of the various codes ("Standard", "SGC0", "Vertebrate Mitochondrial", "SGC1", etc..) and their ids (1, 2, etc...) were taken from the print-form ASN.1 version of the above document (version 4.0 at the time of this writing):

ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt

AA_ALPHABET and AMINO_ACID_CODE.
The translate and trinucleotideFrequency functions.
DNAString, RNAString, and AAString objects.

## ---------------------------------------------------------------------
## THE STANDARD GENETIC CODE
## ---------------------------------------------------------------------

GENETIC_CODE

## Codon ATG is *always* translated to M (Methionine)
GENETIC_CODE[["ATG"]]

## Codons TTG and CTG are "normally" translated to L except when they are
## the first translated codon (a.k.a. start codon or initiation codon),
## in which case they are translated to M:
attr(GENETIC_CODE, "alt_init_codons")
GENETIC_CODE[["TTG"]]
GENETIC_CODE[["CTG"]]

sort(table(GENETIC_CODE))  # the same amino acid can be encoded by 1
                           # to 6 different codons

RNA_GENETIC_CODE
all(GENETIC_CODE == RNA_GENETIC_CODE)  # TRUE

## ---------------------------------------------------------------------
## ALL THE KNOWN GENETIC CODES
## ---------------------------------------------------------------------

GENETIC_CODE_TABLE[1:3 , ]

getGeneticCode("SGC0")  # The Standard Genetic Code, again
stopifnot(identical(getGeneticCode("SGC0"), GENETIC_CODE))

getGeneticCode("SGC1")  # Vertebrate Mitochondrial

getGeneticCode("ascidian", full.search=TRUE)  # Ascidian Mitochondrial

## ---------------------------------------------------------------------
## EXAMINE THE DIFFERENCES BETWEEN THE STANDARD CODE AND A NON-STANDARD
## ONE
## ---------------------------------------------------------------------

idx <- which(GENETIC_CODE != getGeneticCode("SGC1"))
rbind(Standard=GENETIC_CODE[idx], SGC1=getGeneticCode("SGC1")[idx])