# codontable.rb

Path: | lib/bio/data/codontable.rb
Last Update: | Tue Feb 01 03:26:53 +0000 2011

# bio/data/codontable.rb - Codon Table

Copyright: | Copyright (C) 2001, 2004 Toshiaki Katayama <k@bioruby.org>
License: | The Ruby License

$Id:$

## Data source

Data in this class is converted from the NCBI‘s genetic codes page.

     * ((<URL:http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t>))

### Examples

Obtain a codon table No.1 — Standard (Eukaryote)

      table = Bio::CodonTable[1]

Obtain a copy of the codon table No.1 to modify. In this example, reassign a seleno cystein (‘U’) to the ‘tga’ codon.

      table = Bio::CodonTable.copy(1)
      table['tga'] = 'U'

Create a new codon table by your own from the Hash which contains pairs of codon and amino acid. You can also define the table name in the second argument.

      hash = { 'ttt' => 'F', 'ttc' => 'ttc', ... }
      table = Bio::CodonTable.new(hash, "my codon table")

Obtain a translated amino acid by codon.

      table = Bio::CodonTable[1]
      table['ttt']  # => F

Reverse translation of a amino acid into a list of relevant codons.

      table = Bio::CodonTable[1]
      table.revtrans("A")  # => ["gcg", "gct", "gca", "gcc"]

[Validate]