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, full.search=FALSE)

Arguments

Details

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

The Standard Genetic Code (aka 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 1 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 The names of the latter are those of the former where all occurrences of T (thymine) have been replaced by U (uracil).

GENETIC_CODE_TABLE is a data frame with 1 row per known genetic code and the 4 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: The genetic code itself represented in a compact form (i.e. 64 amino acid letters, 1 letter per codon, the codons are assumed to be ordered like in GENETIC_CODE).

getGeneticCode returns a named character vector of length 64 similar to GENETIC_CODE i.e. it contains 1-letter strings in the Amino Acid alphabet (see ?AA_ALPHABET) and its names are identical to names(GENETIC_CODE).

Author(s)

H. Pag<c3><83><c2><a8>s

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 3.9 at the time of this writting):

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

GENETIC_CODE[["ATG"]]  # codon ATG is translated into M (Methionine)

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

## Differences between a non-standard code and the Standard Code:
idx <- which(getGeneticCode("SGC1") != GENETIC_CODE)
rbind(SGC1=getGeneticCode("SGC1")[idx], Standard=GENETIC_CODE[idx])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(Biostrings)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Biostrings/GENETIC_CODE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GENETIC_CODE
> ### Title: The Standard Genetic Code and its known variants
> ### Aliases: GENETIC_CODE RNA_GENETIC_CODE GENETIC_CODE_TABLE
> ###   getGeneticCode
> ### Keywords: utilities data
> 
> ### ** Examples
> 
> ## The Standard Genetic Code:
> 
> GENETIC_CODE
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT CTC CTA CTG 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "*" "W" "L" "L" "L" "L" 
CCT CCC CCA CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG 
"P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" "I" "M" "T" "T" "T" "T" 
AAT AAC AAA AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG 
"N" "N" "K" "K" "S" "S" "R" "R" "V" "V" "V" "V" "A" "A" "A" "A" "D" "D" "E" "E" 
GGT GGC GGA GGG 
"G" "G" "G" "G" 
> 
> GENETIC_CODE[["ATG"]]  # codon ATG is translated into M (Methionine)
[1] "M"
> 
> sort(table(GENETIC_CODE))  # the same amino acid can be encoded by 1
GENETIC_CODE
M W C D E F H K N Q Y * I A G P T V L R S 
1 1 2 2 2 2 2 2 2 2 2 3 3 4 4 4 4 4 6 6 6 
>                            # to 6 different codons
> 
> RNA_GENETIC_CODE
UUU UUC UUA UUG UCU UCC UCA UCG UAU UAC UAA UAG UGU UGC UGA UGG CUU CUC CUA CUG 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "*" "W" "L" "L" "L" "L" 
CCU CCC CCA CCG CAU CAC CAA CAG CGU CGC CGA CGG AUU AUC AUA AUG ACU ACC ACA ACG 
"P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" "I" "M" "T" "T" "T" "T" 
AAU AAC AAA AAG AGU AGC AGA AGG GUU GUC GUA GUG GCU GCC GCA GCG GAU GAC GAA GAG 
"N" "N" "K" "K" "S" "S" "R" "R" "V" "V" "V" "V" "A" "A" "A" "A" "D" "D" "E" "E" 
GGU GGC GGA GGG 
"G" "G" "G" "G" 
> all(GENETIC_CODE == RNA_GENETIC_CODE)  # TRUE
[1] TRUE
> 
> ## All the known genetic codes:
> 
> GENETIC_CODE_TABLE[1:3 , ]
                      name name2 id
1                 Standard  SGC0  1
2 Vertebrate Mitochondrial  SGC1  2
3      Yeast Mitochondrial  SGC2  3
                                                               AAs
1 FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
2 FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
3 FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
> 
> getGeneticCode("SGC0")  # The Standard Genetic Code, again
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT CTC CTA CTG 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "*" "W" "L" "L" "L" "L" 
CCT CCC CCA CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG 
"P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" "I" "M" "T" "T" "T" "T" 
AAT AAC AAA AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG 
"N" "N" "K" "K" "S" "S" "R" "R" "V" "V" "V" "V" "A" "A" "A" "A" "D" "D" "E" "E" 
GGT GGC GGA GGG 
"G" "G" "G" "G" 
> stopifnot(identical(getGeneticCode("SGC0"), GENETIC_CODE))
> 
> getGeneticCode("SGC1")  # Vertebrate Mitochondrial
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT CTC CTA CTG 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "W" "W" "L" "L" "L" "L" 
CCT CCC CCA CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG 
"P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" "M" "M" "T" "T" "T" "T" 
AAT AAC AAA AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG 
"N" "N" "K" "K" "S" "S" "*" "*" "V" "V" "V" "V" "A" "A" "A" "A" "D" "D" "E" "E" 
GGT GGC GGA GGG 
"G" "G" "G" "G" 
> 
> getGeneticCode("ascidian", full.search=TRUE)  # Ascidian Mitochondrial
TTT TTC TTA TTG TCT TCC TCA TCG TAT TAC TAA TAG TGT TGC TGA TGG CTT CTC CTA CTG 
"F" "F" "L" "L" "S" "S" "S" "S" "Y" "Y" "*" "*" "C" "C" "W" "W" "L" "L" "L" "L" 
CCT CCC CCA CCG CAT CAC CAA CAG CGT CGC CGA CGG ATT ATC ATA ATG ACT ACC ACA ACG 
"P" "P" "P" "P" "H" "H" "Q" "Q" "R" "R" "R" "R" "I" "I" "M" "M" "T" "T" "T" "T" 
AAT AAC AAA AAG AGT AGC AGA AGG GTT GTC GTA GTG GCT GCC GCA GCG GAT GAC GAA GAG 
"N" "N" "K" "K" "S" "S" "G" "G" "V" "V" "V" "V" "A" "A" "A" "A" "D" "D" "E" "E" 
GGT GGC GGA GGG 
"G" "G" "G" "G" 
> 
> ## Differences between a non-standard code and the Standard Code:
> idx <- which(getGeneticCode("SGC1") != GENETIC_CODE)
> rbind(SGC1=getGeneticCode("SGC1")[idx], Standard=GENETIC_CODE[idx])
         TGA ATA AGA AGG
SGC1     "W" "M" "*" "*"
Standard "*" "I" "R" "R"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>