GENETIC_CODE           package:Biostrings           R Documentation

The Standard Genetic Code

Description:

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

Usage:

         GENETIC_CODE
         RNA_GENETIC_CODE

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.

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     (thymine) have been replaced by U (uracil).

Author(s):

     H. Pages

References:

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

See Also:

     'AA_ALPHABET', 'AMINO_ACID_CODE', 'translate',
     'trinucleotideFrequency', 'DNAString', 'RNAString', 'AAString'

Examples:

       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

