The Standard Genetic Code and its known variants
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 |
full.search |
By default, only the |
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been replaced by U (uracil).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:
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):
The translate and trinucleotideFrequency
functions.
## ---------------------------------------------------------------------
## 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])Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.