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|
#
# = bio/data/codontable.rb - Codon Table
#
# Copyright:: Copyright (C) 2001, 2004
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
#
# == 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 (defined? @reverse) && @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
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