GENETIC_CODE {Biostrings} | R Documentation

## The Standard Genetic Code and its known variants

### Description

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`.

### Usage

    ## 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)

### Arguments

`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?

### Details

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.

### Value

`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)`.

### Author(s)

H. Pagès

### References

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

### See Also

- `AA_ALPHABET` and `AMINO_ACID_CODE`.

- The `translate` and `trinucleotideFrequency` functions.

- DNAString, RNAString, and AAString objects.

### Examples

    ## ---------------------------------------------------------------------
    ## 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])

[Package Biostrings version 2.56.0 Index]