bio 1.5.1 → 2.0.2

data/gemfiles/Gemfile.travis-jruby1.8

@@ -1,8 +1,6 @@
 source "https://rubygems.org"
 
-gem "rake"
-gem "rdoc"
-
-## disabled because of build error on Travis
-#gem "libxml-ruby"
+gem "rake", "~>10.4"
+# rdoc 4.3.0 requires Ruby >= 1.9.3
+gem "rdoc", "~>4.2.0"
 

data/gemfiles/Gemfile.travis-jruby1.9

@@ -3,6 +3,3 @@ source "https://rubygems.org"
 gem "rake"
 gem "rdoc"
 
-## disabled because of build error on Travis
-#gem "libxml-ruby"
-

data/gemfiles/Gemfile.travis-rbx

@@ -3,9 +3,6 @@ source "https://rubygems.org"
 gem "rake"
 gem "rdoc"
 
-gem "xmlparser"
-gem "libxml-ruby"
-
 platforms :rbx do
   gem 'racc'
   gem 'rubysl', '~> 2.0'

data/gemfiles/Gemfile.travis-ruby1.8

@@ -1,8 +1,6 @@
 source "https://rubygems.org"
 
-gem "rake"
-gem "rdoc"
-
-gem "xmlparser"
-gem "libxml-ruby"
+gem "rake", "~>10.4"
+# rdoc 4.3.0 requires Ruby >= 1.9.3
+gem "rdoc", "~>4.2.0"
 

data/gemfiles/Gemfile.travis-ruby1.9

@@ -3,6 +3,3 @@ source "https://rubygems.org"
 gem "rake"
 gem "rdoc"
 
-gem "xmlparser"
-gem "libxml-ruby"
-

data/gemfiles/Gemfile.windows

@@ -0,0 +1,6 @@
+source "https://rubygems.org"
+
+gem "rake"
+gem "rdoc"
+gem "test-unit"
+

data/gemfiles/prepare-gemspec.rb

@@ -15,6 +15,10 @@ else
   exit(0)
 end
 
+# update bundler to avoid Bundler's bug fixed in the latest version
+$stderr.puts "gem update bundler"
+system("gem update bundler")
+
 $stderr.puts "cd #{gem_dir}"
 Dir.chdir(gem_dir)
 

data/lib/bio.rb

@@ -142,20 +142,10 @@ module Bio
   autoload :Newick,         'bio/db/newick'
   autoload :Nexus,          'bio/db/nexus'
 
-  autoload :PhyloXML,       'bio/db/phyloxml/phyloxml_elements'
-  # Bio::Taxonomy will be moved to other file
-  autoload :Taxonomy,       'bio/db/phyloxml/phyloxml_elements'
-  ## below are described in bio/db/phyloxml/phyloxml_elements.rb
-  #module PhyloXML
-  #  autoload :Parser,       'bio/db/phyloxml/phyloxml_parser'
-  #  autoload :Writer,       'bio/db/phyloxml/phyloxml_writer'
-  #end
-
   ### IO interface modules
 
   autoload :Registry,       'bio/io/registry'
   autoload :Fetch,          'bio/io/fetch'
-  autoload :SQL,            'bio/io/sql'
   autoload :FlatFile,       'bio/io/flatfile'
   autoload :FlatFileIndex,  'bio/io/flatfile/index' # chage to FlatFile::Index ?
   ## below are described in bio/io/flatfile/index.rb

data/lib/bio/appl/blast/genomenet.rb

@@ -102,7 +102,7 @@ module Bio::Blast::Remote
         dbdescs = {}
         key = nil
         host = Bio::Blast::Remote::Genomenet::Host
-        http = Bio::Command.new_http(host)
+        http = Bio::Command.new_https(host)
         result = http.get('/tools/blast/')
         #p result.body
         result.body.each_line do |line|
@@ -211,7 +211,7 @@ module Bio::Blast::Remote
       end
 
       begin
-        http = Bio::Command.new_http(host)
+        http = Bio::Command.new_https(host)
         http.open_timeout = 300
         http.read_timeout = 600
         result = Bio::Command.http_post_form(http, path, form)
@@ -243,10 +243,10 @@ module Bio::Blast::Remote
         end
 
         # workaround 2005.08.12 + 2011.01.27 + 2011.7.22
-        if /\<A +HREF=\"(http\:\/\/[\-\.a-z0-9]+\.genome\.jp)?(\/tmp\/[^\"]+)\"\>Show all result\<\/A\>/i =~ @output.to_s then
+        if /\<A +HREF=\"(https?\:\/\/[\-\.a-z0-9]+\.genome\.jp)?(\/tmp\/[^\"]+)\"\>Show all result\<\/A\>/i =~ @output.to_s then
           all_prefix = $1
           all_path = $2
-          all_prefix = "http://#{Host}" if all_prefix.to_s.empty?
+          all_prefix = "https://#{Host}" if all_prefix.to_s.empty?
           all_uri = all_prefix + all_path
           @output = Bio::Command.read_uri(all_uri)
           case all_path

data/lib/bio/appl/blast/report.rb

@@ -43,18 +43,20 @@ class Report
   #--
   # require lines moved here to avoid circular require
   #++
-  require 'bio/appl/blast/xmlparser'
   require 'bio/appl/blast/rexml'
   require 'bio/appl/blast/format8'
 
+  #--
+  # loading bio-blast-xmlparser plugin if available
+  #++
+  begin
+    require 'bio-blast-xmlparser'
+  rescue LoadError
+  end
+
   # for Bio::FlatFile support (only for XML data)
   DELIMITER = RS = "</BlastOutput>\n"
 
-  # Specify to use XMLParser to parse XML (-m 7) output.
-  def self.xmlparser(data)
-    self.new(data, :xmlparser)
-  end
-
   # Specify to use REXML to parse XML (-m 7) output.
   def self.rexml(data)
     self.new(data, :rexml)
@@ -67,7 +69,7 @@ class Report
 
   def auto_parse(data)
     if /<?xml/.match(data[/.*/])
-      if defined?(XMLParser)
+      if defined? xmlparser_parse
         xmlparser_parse(data)
         @reports = blastxml_split_reports
       else
@@ -87,7 +89,11 @@ class Report
     @parameters = {}
     case parser
     when :xmlparser		# format 7
-      xmlparser_parse(data)
+      if defined? xmlparser_parse
+        xmlparser_parse(data)
+      else
+        raise NameError, "xmlparser_parse does not defined"
+      end
       @reports = blastxml_split_reports
     when :rexml		# format 7
       rexml_parse(data)
@@ -383,6 +389,32 @@ class Report
   attr_reader :reports
  
   private
+  # set parameter of the key as val
+  def xml_set_parameter(key, val)
+    #labels = { 
+    #  'matrix'       => 'Parameters_matrix',
+    #  'expect'       => 'Parameters_expect',
+    #  'include'      => 'Parameters_include',
+    #  'sc-match'     => 'Parameters_sc-match',
+    #  'sc-mismatch'  => 'Parameters_sc-mismatch',
+    #  'gap-open'     => 'Parameters_gap-open',
+    #  'gap-extend'   => 'Parameters_gap-extend',
+    #  'filter'       => 'Parameters_filter',
+    #  'pattern'      => 'Parameters_pattern',
+    #  'entrez-query' => 'Parameters_entrez-query',
+    #}
+    k = key.sub(/\AParameters\_/, '')
+    @parameters[k] =
+      case k
+      when 'expect', 'include'
+        val.to_f
+      when /\Agap\-/, /\Asc\-/
+        val.to_i
+      else
+        val
+      end
+  end
+
   # (private method)
   # In new BLAST XML (blastall >= 2.2.14), results of multiple queries
   # are stored in <Iteration>. This method splits iterations into

data/lib/bio/appl/fasta/format10.rb

@@ -94,8 +94,9 @@ class Report
     # header lines - brief list of the hits
     if list_start = data.index("\nThe best scores are") then
       data = data[(list_start + 1)..-1]
-      data.sub!(/(.*)\n\n>>>/m, '')
+      data.sub!(/(.*?)\n\n>>>/m, '')
       @list = $1
+      data.sub!(/>>><<<(.*)$/m, '')
     else
       if list_start = data.index(/\n!!\s+/) then
         data = data[list_start..-1]

data/lib/bio/command.rb

@@ -791,6 +791,16 @@ module Command
     end
   end
 
+  # Same as:
+  #   h = Bio::Command.new_http(address, port)
+  #   h.use_ssl = true
+  #   h
+  def new_https(address, port = 443)
+    connection = new_http(address, port)
+    connection.use_ssl = true
+    connection
+  end
+
   # Same as:
   #  http = Net::HTTP.new(...); http.post_form(path, params)
   # and 

data/lib/bio/data/codontable.rb

@@ -51,10 +51,15 @@ class CodonTable
   def self.[](i)
     hash = TABLES[i]
     raise "ERROR: Unknown codon table No.#{i}" unless hash
+    if AMBIGUITY_CODON_TABLES != nil
+      atable = AMBIGUITY_CODON_TABLES[i]
+    else
+      atable = nil
+    end
     definition = DEFINITIONS[i]
     start = STARTS[i]
     stop = STOPS[i]
-    self.new(hash, definition, start, stop)
+    self.new(hash, definition, start, stop, atable)
   end
 
   # Similar to Bio::CodonTable[num] but returns a copied codon table.
@@ -70,8 +75,13 @@ class CodonTable
   #
   # 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 = [])
+  def initialize(hash, definition = nil, start = [], stop = [], atable = nil)
     @table = hash
+    if atable == nil
+      @atable = gen_ambiguity_map(hash)
+    else
+      @atable = atable
+    end
     @definition = definition
     @start = start
     @stop = stop.empty? ? generate_stop : stop
@@ -87,10 +97,55 @@ class CodonTable
   # codons respectively.
   attr_accessor :start, :stop
 
+  # Compute possible ambiguity nucleotide code to amino acid conversion
+  # the codon is defined when all decomposed codon translates to the
+  # same amino acid / stop codon
+  def gen_ambiguity_map(hash)
+    nucleotide_sets={
+      'a'       => ['a'],
+      't'       => ['t'],
+      'g'       => ['g'],
+      'c'       => ['c'],
+
+      'y'       => ['t','c'],
+      'r'       => ['a','g'],
+      'w'       => ['a','t'],
+      's'       => ['g','c'],
+      'k'       => ['t','g'],
+      'm'       => ['a','c'],
+
+      'b'       => ['t','g','c'],
+      'd'       => ['a','t','g'],
+      'h'       => ['a','t','c'],
+      'v'       => ['a','g','c'],
+
+      'n'       => ['a','t','g','c'],
+    }
+    atable=Hash.new
+    nucleotide_sets.keys.each{|n1|
+      nucleotide_sets.keys.each{|n2|
+        nucleotide_sets.keys.each{|n3|
+          a = Array.new
+          nucleotide_sets[n1].each{|c1|
+            nucleotide_sets[n2].each{|c2|
+              nucleotide_sets[n3].each{|c3|
+                a << hash["#{c1}#{c2}#{c3}"]
+              }
+            }
+          }
+          a.uniq!
+          atable["#{n1}#{n2}#{n3}"] = a.to_a[0] if a.size== 1
+        }
+      }
+    }
+    atable
+  end
+
   # 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]
+    @atable=gen_ambiguity_map(@table) if @atable == nil
+    @atable[codon]
   end
 
   # Modify the codon table.  Use with caution as it may break hard coded
@@ -107,6 +162,7 @@ class CodonTable
   #
   def []=(codon, aa)
     @table[codon] = aa
+    @atable = nil
   end
 
   # Iterates on codon table hash.
@@ -625,3 +681,43 @@ end # CodonTable
 
 end # module Bio
 
+module Bio
+class CodonTable
+AMBIGUITY_CODON_TABLES = {
+1 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+2 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"*", "agt"=>"S", "agg"=>"*", "agc"=>"S", "agy"=>"S", "agr"=>"*", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+3 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"T", "ctt"=>"T", "ctg"=>"T", "ctc"=>"T", "cty"=>"T", "ctr"=>"T", "ctw"=>"T", "cts"=>"T", "ctk"=>"T", "ctm"=>"T", "ctb"=>"T", "ctd"=>"T", "cth"=>"T", "ctv"=>"T", "ctn"=>"T", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+4 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+5 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"S", "agt"=>"S", "agg"=>"S", "agc"=>"S", "agy"=>"S", "agr"=>"S", "agw"=>"S", "ags"=>"S", "agk"=>"S", "agm"=>"S", "agb"=>"S", "agd"=>"S", "agh"=>"S", "agv"=>"S", "agn"=>"S", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+6 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"Q", "tat"=>"Y", "tag"=>"Q", "tac"=>"Y", "tay"=>"Y", "tar"=>"Q", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yaa"=>"Q", "yag"=>"Q", "yar"=>"Q", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+9 =>
+{"aaa"=>"N", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aaw"=>"N", "aam"=>"N", "aah"=>"N", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"S", "agt"=>"S", "agg"=>"S", "agc"=>"S", "agy"=>"S", "agr"=>"S", "agw"=>"S", "ags"=>"S", "agk"=>"S", "agm"=>"S", "agb"=>"S", "agd"=>"S", "agh"=>"S", "agv"=>"S", "agn"=>"S", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+10 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"C", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgw"=>"C", "tgm"=>"C", "tgh"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+11 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+12 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"S", "ctc"=>"L", "cty"=>"L", "ctw"=>"L", "ctm"=>"L", "cth"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+13 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"G", "agt"=>"S", "agg"=>"G", "agc"=>"S", "agy"=>"S", "agr"=>"G", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "rga"=>"G", "rgg"=>"G", "rgr"=>"G"}, 
+14 =>
+{"aaa"=>"N", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aaw"=>"N", "aam"=>"N", "aah"=>"N", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"S", "agt"=>"S", "agg"=>"S", "agc"=>"S", "agy"=>"S", "agr"=>"S", "agw"=>"S", "ags"=>"S", "agk"=>"S", "agm"=>"S", "agb"=>"S", "agd"=>"S", "agh"=>"S", "agv"=>"S", "agn"=>"S", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"Y", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "taw"=>"Y", "tam"=>"Y", "tah"=>"Y", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+15 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"Q", "tac"=>"Y", "tay"=>"Y", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yag"=>"Q", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+16 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"L", "tac"=>"Y", "tay"=>"Y", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "twg"=>"L", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+21 =>
+{"aaa"=>"N", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aaw"=>"N", "aam"=>"N", "aah"=>"N", "ata"=>"M", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atr"=>"M", "aga"=>"S", "agt"=>"S", "agg"=>"S", "agc"=>"S", "agy"=>"S", "agr"=>"S", "agw"=>"S", "ags"=>"S", "agk"=>"S", "agm"=>"S", "agb"=>"S", "agd"=>"S", "agh"=>"S", "agv"=>"S", "agn"=>"S", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"W", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tgr"=>"W", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L"}, 
+22 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"L", "tac"=>"Y", "tay"=>"Y", "tta"=>"L", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "ttr"=>"L", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"*", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcs"=>"S", "tck"=>"S", "tcb"=>"S", "tra"=>"*", "twg"=>"L", "tsa"=>"*", "tma"=>"*", "tva"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "yta"=>"L", "ytg"=>"L", "ytr"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+23 =>
+{"aaa"=>"K", "aat"=>"N", "aag"=>"K", "aac"=>"N", "aay"=>"N", "aar"=>"K", "ata"=>"I", "att"=>"I", "atg"=>"M", "atc"=>"I", "aty"=>"I", "atw"=>"I", "atm"=>"I", "ath"=>"I", "aga"=>"R", "agt"=>"S", "agg"=>"R", "agc"=>"S", "agy"=>"S", "agr"=>"R", "aca"=>"T", "act"=>"T", "acg"=>"T", "acc"=>"T", "acy"=>"T", "acr"=>"T", "acw"=>"T", "acs"=>"T", "ack"=>"T", "acm"=>"T", "acb"=>"T", "acd"=>"T", "ach"=>"T", "acv"=>"T", "acn"=>"T", "taa"=>"*", "tat"=>"Y", "tag"=>"*", "tac"=>"Y", "tay"=>"Y", "tar"=>"*", "tta"=>"*", "ttt"=>"F", "ttg"=>"L", "ttc"=>"F", "tty"=>"F", "tga"=>"*", "tgt"=>"C", "tgg"=>"W", "tgc"=>"C", "tgy"=>"C", "tca"=>"S", "tct"=>"S", "tcg"=>"S", "tcc"=>"S", "tcy"=>"S", "tcr"=>"S", "tcw"=>"S", "tcs"=>"S", "tck"=>"S", "tcm"=>"S", "tcb"=>"S", "tcd"=>"S", "tch"=>"S", "tcv"=>"S", "tcn"=>"S", "tra"=>"*", "twa"=>"*", "tka"=>"*", "tda"=>"*", "gaa"=>"E", "gat"=>"D", "gag"=>"E", "gac"=>"D", "gay"=>"D", "gar"=>"E", "gta"=>"V", "gtt"=>"V", "gtg"=>"V", "gtc"=>"V", "gty"=>"V", "gtr"=>"V", "gtw"=>"V", "gts"=>"V", "gtk"=>"V", "gtm"=>"V", "gtb"=>"V", "gtd"=>"V", "gth"=>"V", "gtv"=>"V", "gtn"=>"V", "gga"=>"G", "ggt"=>"G", "ggg"=>"G", "ggc"=>"G", "ggy"=>"G", "ggr"=>"G", "ggw"=>"G", "ggs"=>"G", "ggk"=>"G", "ggm"=>"G", "ggb"=>"G", "ggd"=>"G", "ggh"=>"G", "ggv"=>"G", "ggn"=>"G", "gca"=>"A", "gct"=>"A", "gcg"=>"A", "gcc"=>"A", "gcy"=>"A", "gcr"=>"A", "gcw"=>"A", "gcs"=>"A", "gck"=>"A", "gcm"=>"A", "gcb"=>"A", "gcd"=>"A", "gch"=>"A", "gcv"=>"A", "gcn"=>"A", "caa"=>"Q", "cat"=>"H", "cag"=>"Q", "cac"=>"H", "cay"=>"H", "car"=>"Q", "cta"=>"L", "ctt"=>"L", "ctg"=>"L", "ctc"=>"L", "cty"=>"L", "ctr"=>"L", "ctw"=>"L", "cts"=>"L", "ctk"=>"L", "ctm"=>"L", "ctb"=>"L", "ctd"=>"L", "cth"=>"L", "ctv"=>"L", "ctn"=>"L", "cga"=>"R", "cgt"=>"R", "cgg"=>"R", "cgc"=>"R", "cgy"=>"R", "cgr"=>"R", "cgw"=>"R", "cgs"=>"R", "cgk"=>"R", "cgm"=>"R", "cgb"=>"R", "cgd"=>"R", "cgh"=>"R", "cgv"=>"R", "cgn"=>"R", "cca"=>"P", "cct"=>"P", "ccg"=>"P", "ccc"=>"P", "ccy"=>"P", "ccr"=>"P", "ccw"=>"P", "ccs"=>"P", "cck"=>"P", "ccm"=>"P", "ccb"=>"P", "ccd"=>"P", "cch"=>"P", "ccv"=>"P", "ccn"=>"P", "ytg"=>"L", "mga"=>"R", "mgg"=>"R", "mgr"=>"R"}, 
+}
+end #CodonTable
+end #Bio

data/lib/bio/db/aaindex.rb

@@ -7,12 +7,11 @@
 #              Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
 #
 # == Description
 #
 # Classes for Amino Acid Index Database (AAindex and AAindex2).
-# * AAindex Manual: http://www.genome.jp/dbget-bin/show_man?aaindex
+# * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
 #
 # == Examples
 #
@@ -40,7 +39,38 @@ require "matrix"
 
 module Bio
 
-  # Super class for AAindex1 and AAindex2
+  # == Description
+  #
+  # Bio::AAindex is the super class of Bio::AAindex1 and Bio::AAindex2,
+  # parser classes for AAindex Amino Acid Index Database.
+  # * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
+  #
+  # Except Bio::AAindex.auto, do not use this class directly.
+  # Methods of this super class is used from AAindex1 and AAindex2 classes.
+  #
+  # == Examples
+  #
+  #  # auto-detection of data format
+  #  aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")
+  #  aax2 = Bio::AAindex.auto("DAYM780301.aaindex2")
+  #
+  #  # Example of Bio::AAindex1 class
+  #  aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
+  #  aax1.entry_id
+  #  aax1.index
+  #
+  #  # Example of Bio::AAindex2 class
+  #  aax2 = Bio::AAindex2.new("DAYM780301.aaindex2")
+  #  aax2.entry_id
+  #  aax2.matrix
+  #  aax2.matrix[2,2]
+  #  aax2.matrix('R', 'A')
+  #  aax2['R', 'A']
+  #
+  # == References
+  #
+  # * http://www.genome.jp/aaindex/
+  #
   class AAindex < KEGGDB
 
     # Delimiter
@@ -136,7 +166,25 @@ module Bio
   end
 
 
-  # Class for AAindex1 format.
+  # == Description
+  #
+  # Parser class for AAindex1, Amino Acid Index Database.
+  # * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
+  #
+  # == Examples
+  #
+  #  # auto-detection of data format by using Bio::AAindex class
+  #  aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")
+  #
+  #  # parse a file and get contents
+  #  aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
+  #  aax1.entry_id
+  #  aax1.index
+  #
+  # == References
+  #
+  # * http://www.genome.jp/aaindex/
+  #
   class AAindex1 < AAindex
 
     def initialize(entry)
@@ -211,7 +259,28 @@ module Bio
   end
 
 
-  # Class for AAindex2 format.
+  # == Description
+  #
+  # Parser class for AAindex2, Amino Acid Index Database.
+  # * AAindex Help: https://www.genome.jp/aaindex/aaindex_help.html
+  #
+  # == Examples
+  #
+  #  # auto-detection of data format by using Bio::AAindex class
+  #  aax2 = Bio::AAindex.auto("DAYM780301.aaindex2")
+  #
+  #  # parse a file and get contents
+  #  aax2 = Bio::AAindex2.new("DAYM780301.aaindex2")
+  #  aax2.entry_id
+  #  aax2.matrix
+  #  aax2.matrix[2,2]
+  #  aax2.matrix('R', 'A')
+  #  aax2['R', 'A']
+  #
+  # == References
+  #
+  # * http://www.genome.jp/aaindex/
+  #
   class AAindex2 < AAindex
 
     def initialize(entry)