jandot-bio 1.2.1

data/lib/bio/data/codontable.rb

@@ -0,0 +1,722 @@
+#
+# = bio/data/codontable.rb - Codon Table
+#
+# Copyright::	Copyright (C) 2001, 2004
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	The Ruby License
+#
+# $Id: codontable.rb,v 0.18 2007/04/05 23:35:40 trevor Exp $
+#
+# == 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"]
+#
+
+module Bio
+
+class CodonTable
+
+  # Select a codon table by number.  This method will return one of the
+  # hard coded codon tables in this class as a Bio::CodonTable object.
+  def self.[](i)
+    hash = TABLES[i]
+    raise "ERROR: Unknown codon table No.#{i}" unless hash
+    definition = DEFINITIONS[i]
+    start = STARTS[i]
+    stop = STOPS[i]
+    self.new(hash, definition, start, stop)
+  end
+
+  # Similar to Bio::CodonTable[num] but returns a copied codon table.
+  # You can modify the codon table without influencing hard coded tables.
+  def self.copy(i)
+    ct = self[i]
+    return Marshal.load(Marshal.dump(ct))
+  end
+
+  # Create your own codon table by giving a Hash table of codons and relevant
+  # amino acids.  You can also able to define the table's name as a second
+  # argument.
+  #
+  # Two Arrays 'start' and 'stop' can be specified which contains a list of
+  # start and stop codons used by 'start_codon?' and 'stop_codon?' methods.
+  def initialize(hash, definition = nil, start = [], stop = [])
+    @table = hash
+    @definition = definition
+    @start = start
+    @stop = stop.empty? ? generate_stop : stop
+  end
+
+  # Accessor methods for a Hash of the currently selected codon table.
+  attr_accessor :table
+
+  # Accessor methods for the name of the currently selected table.
+  attr_accessor :definition
+
+  # Accessor methods for an Array which contains a list of start or stop
+  # codons respectively.
+  attr_accessor :start, :stop
+
+  # Translate a codon into a relevant amino acid.  This method is used for
+  # translating a DNA sequence into amino acid sequence.
+  def [](codon)
+    @table[codon]
+  end
+
+  # Modify the codon table.  Use with caution as it may break hard coded
+  # tables.  If you want to modify existing table, you should use copy
+  # method instead of [] method to generate CodonTable object to be modified.
+  #
+  #   # This is OK.
+  #   table = Bio::CodonTable.copy(1)
+  #   table['tga'] = 'U'
+  #
+  #   # Not recommended as it overrides the hard coded table
+  #   table = Bio::CodonTable[1]
+  #   table['tga'] = 'U'
+  #
+  def []=(codon, aa)
+    @table[codon] = aa
+  end
+
+  # Iterates on codon table hash.
+  #
+  #   table = Bio::CodonTable[1]
+  #   table.each do |codon, aa|
+  #     puts "#{codon} -- #{aa}"
+  #    end
+  #
+  def each(&block)
+    @table.each(&block)
+  end
+
+  # Reverse translation of a amino acid into a list of relevant codons.
+  #
+  #   table = Bio::CodonTable[1]
+  #   table.revtrans("A")	# => ["gcg", "gct", "gca", "gcc"]
+  #
+  def revtrans(aa)
+    unless @reverse
+      @reverse = {}
+      @table.each do |k, v|
+        @reverse[v] ||= []
+        @reverse[v] << k
+      end
+    end
+    @reverse[aa.upcase]
+  end
+
+  # Returns true if the codon is a start codon in the currently selected
+  # codon table, otherwise false.
+  def start_codon?(codon)
+    @start.include?(codon.downcase)
+  end
+
+  # Returns true if the codon is a stop codon in the currently selected
+  # codon table, otherwise false.
+  def stop_codon?(codon)
+    @stop.include?(codon.downcase)
+  end
+
+  def generate_stop
+    list = []
+    @table.each do |codon, aa|
+      if aa == '*'
+        list << codon
+      end
+    end
+    return list
+  end
+  private :generate_stop
+
+  DEFINITIONS = {
+
+    1	=> "Standard (Eukaryote)",
+    2	=> "Vertebrate Mitochondrial",
+    3	=> "Yeast Mitochondorial",
+    4	=> "Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma",
+    5	=> "Invertebrate Mitochondrial",
+    6	=> "Ciliate Macronuclear and Dasycladacean",
+    9	=> "Echinoderm Mitochondrial",
+    10	=> "Euplotid Nuclear",
+    11	=> "Bacteria",
+    12	=> "Alternative Yeast Nuclear",
+    13	=> "Ascidian Mitochondrial",
+    14	=> "Flatworm Mitochondrial",
+    15	=> "Blepharisma Macronuclear",
+    16	=> "Chlorophycean Mitochondrial",
+    21	=> "Trematode Mitochondrial",
+    22	=> "Scenedesmus obliquus mitochondrial",
+    23	=> "Thraustochytrium Mitochondrial",
+
+  }
+
+
+  STARTS = {
+    1	=> %w(ttg ctg atg gtg),		# gtg added (cf. NCBI #SG1 document)
+    2	=> %w(att atc ata atg gtg),
+    3	=> %w(ata atg),
+    4	=> %w(tta ttg ctg att atc ata atg gtg),
+    5	=> %w(ttg att atc ata atg gtg),
+    6	=> %w(atg),
+    9	=> %w(atg gtg),
+    10	=> %w(atg),
+    11	=> %w(ttg ctg att atc ata atg gtg),
+    12	=> %w(ctg atg),
+    13	=> %w(atg),
+    14	=> %w(atg),
+    15	=> %w(atg),
+    16	=> %w(atg),
+    21	=> %w(atg gtg),
+    22	=> %w(atg),
+    23	=> %w(att atg gtg),
+  }
+
+
+  STOPS = {
+    1	=> %w(taa tag tga),
+    2	=> %w(taa tag aga agg),
+    3	=> %w(taa tag),
+    4	=> %w(taa tag),
+    5	=> %w(taa tag),
+    6	=> %w(tga),
+    9	=> %w(taa tag),
+    10	=> %w(taa tag),
+    11	=> %w(taa tag tga),
+    12	=> %w(taa tag tga),
+    13	=> %w(taa tag),
+    14	=> %w(tag),
+    15	=> %w(taa tga),
+    16	=> %w(taa tga),
+    21	=> %w(taa tag),
+    22	=> %w(tca taa tga),
+    23	=> %w(tta taa tag tga),
+  }
+
+
+  TABLES = {
+
+    # codon table 1
+    1 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 2
+    2 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'M', 'aca' => 'T', 'aaa' => 'K', 'aga' => '*',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => '*',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+
+    # codon table 3
+    3 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'T', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'T', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'T', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'T', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'M', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 4
+    4 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 5
+    5 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'M', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'S',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'S',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 6
+    6 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => 'Q', 'tga' => '*',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => 'Q', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 9
+    9 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'N', 'aga' => 'S',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'S',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 10
+    10 => {
+
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'C',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 11
+    11 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat'	=> 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac'	=> 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa'	=> '*', 'tga' => '*',
+      'ttg' => 'L', 'tcg' => 'S', 'tag'	=> '*', 'tgg' => 'W',
+       	
+      'ctt' => 'L', 'cct' => 'P', 'cat'	=> 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac'	=> 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa'	=> 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag'	=> 'Q', 'cgg' => 'R',
+       	
+      'att' => 'I', 'act' => 'T', 'aat'	=> 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac'	=> 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa'	=> 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag'	=> 'K', 'agg' => 'R',
+       	
+      'gtt' => 'V', 'gct' => 'A', 'gat'	=> 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac'	=> 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa'	=> 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag'	=> 'E', 'ggg' => 'G',
+    },
+
+    # codon table 12
+    12 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'S', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 13
+    13 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'M', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'G',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'G',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 14
+    14 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => 'Y', 'tga' => 'W',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'N', 'aga' => 'S',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'S',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 15
+    15 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => 'Q', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 16
+    16 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => 'L', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 21
+    21 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'W',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'M', 'aca' => 'T', 'aaa' => 'N', 'aga' => 'S',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'S',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 22
+    22 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => 'L', 'tca' => '*', 'taa' => '*', 'tga' => '*',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => 'L', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+    # codon table 23
+    23 => {
+      'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+      'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+      'tta' => '*', 'tca' => 'S', 'taa' => '*', 'tga' => '*',
+      'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+      'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+      'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+      'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+      'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+      'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+      'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+      'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+      'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+      'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+      'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+      'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+      'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+    },
+
+  }
+
+end # CodonTable
+
+end # module Bio
+
+
+if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  puts "### Bio::CodonTable[1]"
+  p ct1 = Bio::CodonTable[1]
+
+  puts ">>> Bio::CodonTable#table"
+  p ct1.table
+
+  puts ">>> Bio::CodonTable#each"
+  ct1.each do |codon, aa|
+    puts "#{codon} -- #{aa}"
+  end
+
+  puts ">>> Bio::CodonTable#definition"
+  p ct1.definition
+
+  puts ">>> Bio::CodonTable#['atg']"
+  p ct1['atg']
+
+  puts ">>> Bio::CodonTable#revtrans('A')"
+  p ct1.revtrans('A')
+
+  puts ">>> Bio::CodonTable#start_codon?('atg')"
+  p ct1.start_codon?('atg')
+  
+  puts ">>> Bio::CodonTable#start_codon?('aaa')"
+  p ct1.start_codon?('aaa')
+
+  puts ">>> Bio::CodonTable#stop_codon?('tag')"
+  p ct1.stop_codon?('tag')
+  
+  puts ">>> Bio::CodonTable#stop_codon?('aaa')"
+  p ct1.stop_codon?('aaa')
+
+  puts ">>> ct1_copy = Bio::CodonTable.copy(1)"
+  p ct1_copy = Bio::CodonTable.copy(1)
+  puts ">>> ct1_copy['tga'] = 'U'"
+  p ct1_copy['tga'] = 'U'
+  puts " orig : #{ct1['tga']}"
+  puts " copy : #{ct1_copy['tga']}"
+
+
+  puts "### ct = Bio::CodonTable.new(hash, definition)"
+  hash = {
+    'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+    'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+    'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'U',
+    'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+    'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+    'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+    'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+    'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+    'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+    'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+    'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+    'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+    'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+    'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+    'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+    'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+  }
+  my_ct = Bio::CodonTable.new(hash, "my codon table")
+
+  puts ">>> ct.definition"
+  puts my_ct.definition
+
+  puts ">>> ct.definition=(str)"
+  my_ct.definition = "selenoproteins (Eukaryote)"
+  puts my_ct.definition
+
+  puts ">>> ct['tga']"
+  puts my_ct['tga']
+
+  puts ">>> ct.revtrans('U')"
+  puts my_ct.revtrans('U')
+
+  puts ">>> ct.stop_codon?('tga')"
+  puts my_ct.stop_codon?('tga')
+
+  puts ">>> ct.stop_codon?('tag')"
+  puts my_ct.stop_codon?('tag')
+
+end
+