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2 # Copyright (c) 2003-2005 The Regents of the University of California.
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3 # Copyright (c) 2005 Gavin E. Crooks
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4
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5 # This software is distributed under the MIT Open Source License.
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6 # <http://www.opensource.org/licenses/mit-license.html>
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7 #
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8 # Permission is hereby granted, free of charge, to any person obtaining a
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9 # copy of this software and associated documentation files (the "Software"),
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10 # to deal in the Software without restriction, including without limitation
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11 # the rights to use, copy, modify, merge, publish, distribute, sublicense,
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12 # and/or sell copies of the Software, and to permit persons to whom the
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13 # Software is furnished to do so, subject to the following conditions:
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14 #
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15 # The above copyright notice and this permission notice shall be included
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16 # in all copies or substantial portions of the Software.
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17 #
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18 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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19 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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20 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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21 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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22 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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23 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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24 # THE SOFTWARE.
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25
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26 """ Popular color codings for nucleic and amino acids.
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27
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28 Classes:
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29 ColorScheme -- A color scheme
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30 ColorGroup
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31
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32
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33 Generic
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34 monochrome
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35
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36 Nucleotides
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37 nucleotide
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38 base pairing
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39
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40 Amino Acid
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41 hydrophobicity
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42 chemistry
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43 charge
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44 taylor
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45
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46 Status : Beta - Needs documentation.
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47
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48 """
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49 # Good online references include bioruby and the JalView alignment editor.
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50 # Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),
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51 # "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7
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52 # http://www.jalview.org
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53
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54 import sys
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55
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56 from corebio import seq
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57 from color import Color
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58 codon_alphabetU=['AAA', 'AAU', 'AAC', 'AAG', 'AUA', 'AUU', 'AUC', 'AUG', 'ACA', 'ACU', 'ACC', 'ACG', 'AGA', 'AGU', 'AGC', 'AGG', 'UAA', 'UAU', 'UAC', 'UAG', 'UUA', 'UUU', 'UUC', 'UUG', 'UCA', 'UCU', 'UCC', 'UCG', 'UGA', 'UGU', 'UGC', 'UGG', 'CAA', 'CAU', 'CAC', 'CAG', 'CUA', 'CUU', 'CUC', 'CUG', 'CCA', 'CCU', 'CCC', 'CCG', 'CGA', 'CGU', 'CGC', 'CGG', 'GAA', 'GAU', 'GAC', 'GAG', 'GUA', 'GUU', 'GUC', 'GUG', 'GCA', 'GCU', 'GCC', 'GCG', 'GGA', 'GGU', 'GGC', 'GGG']
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59 codon_alphabetT=['AAA', 'AAT', 'AAC', 'AAG', 'ATA', 'ATT', 'ATC', 'ATG', 'ACA', 'ACT', 'ACC', 'ACG', 'AGA', 'AGT', 'AGC', 'AGG', 'TAA', 'TAT', 'TAC', 'TAG', 'TTA', 'TTT', 'TTC', 'TTG', 'TCA', 'TCT', 'TCC', 'TCG', 'TGA', 'TGT', 'TGC', 'TGG', 'CAA', 'CAT', 'CAC', 'CAG', 'CTA', 'CTT', 'CTC', 'CTG', 'CCA', 'CCT', 'CCC', 'CCG', 'CGA', 'CGT', 'CGC', 'CGG', 'GAA', 'GAT', 'GAC', 'GAG', 'GTA', 'GTT', 'GTC', 'GTG', 'GCA', 'GCT', 'GCC', 'GCG', 'GGA', 'GGT', 'GGC', 'GGG']
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60
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61 class ColorScheme(object):
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62 """ A coloring of an alphabet.
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63
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64 title : string -- A human readable description
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65 defualt_color : Color --
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66 groups : list of color groups
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67 alphabet : string -- The set of colored symbols
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68 color -- A map between a symbol and a Coloring
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69
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70
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71 """
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72
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73 def __init__(self,
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74 groups = [],
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75 title = "",
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76 description = "",
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77 default_color = "black",
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78 alphabet = seq.generic_alphabet) :
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79 """ """
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80 self.title= title
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81 self.description = description
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82 self.default_color = Color.from_string(default_color)
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83 self.groups = groups
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84 self.alphabet = alphabet
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85 #print >> sys.stderr, groups
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86 altype="codons"
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87 #print >> sys.stderr,altype
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88 #if(alphabet==codon_alphabet):
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89 #print >> sys.stderr,"haleyulia it works"
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90
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91 color = {}
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92 #print >> sys.stderr, groups
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93 if(alphabet!=codon_alphabetT and alphabet!=codon_alphabetU):
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94 for cg in groups :
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95 #print >> sys.stderr, cg
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96 for s in cg.symbols :
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97 color[s] = cg.color
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98 #print >> sys.stderr, s
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99 #print >> sys.stderr, cg
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100 if s not in alphabet :
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101 raise KeyError("Colored symbol does not exist in alphabet.")
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102 else:
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103 for cg in groups :
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104 #print >> sys.stderr, cg
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105 color[cg.symbols] = cg.color
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106 #print >> sys.stderr, cg.symbols
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107 self._color = color
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108
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109 def color(self, symbol) :
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110 if symbol in self._color :
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111 return self._color[symbol]
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112 return self.default_color
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113
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114 class ColorGroup(object) :
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115 """Associate a group of symbols with a color"""
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116 def __init__(self, symbols, color, description=None) :
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117 self.symbols = symbols
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118 self.color = Color.from_string(color)
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119 self.description = description
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120
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121
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122
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123 monochrome = ColorScheme([]) # This list intentionally left blank
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124
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125 # From makelogo
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126 nucleotide = ColorScheme([
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127 ColorGroup("G", "orange"),
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128 ColorGroup("TU", "red"),
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129 ColorGroup("C", "blue"),
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130 ColorGroup("A", "green")
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131 ])
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132
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133 base_pairing = ColorScheme([
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134 ColorGroup("TAU", "darkorange", "Weak (2 Watson-Crick hydrogen bonds)"),
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135 ColorGroup("GC", "blue", "Strong (3 Watson-Crick hydrogen bonds)")],
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136 )
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137
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138
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139 hydrophobicity = ColorScheme([
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140 ColorGroup( "RKDENQ", "black", "hydrophobic"),
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141 ColorGroup( "SGHTAP", "green", "neutral" ),
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142 ColorGroup( "YVMCLFIW", "blue", "hydrophilic") ],
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143 alphabet = seq.unambiguous_protein_alphabet
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144 )
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145
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146 # from makelogo
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147 chemistry = ColorScheme([
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148 ColorGroup( "GSTYC", "green", "polar"),
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149 ColorGroup( "NQ", "purple", "neutral"),
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150 ColorGroup( "KRH", "blue", "basic"),
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151 ColorGroup( "DE", "red", "acidic"),
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152 ColorGroup("PAWFLIMV", "black", "hydrophobic") ],
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153 alphabet = seq.unambiguous_protein_alphabet
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154 )
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155
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156
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157 codonsU = ColorScheme([
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158 ColorGroup( 'CAT', '#00FFFF'),
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159 ColorGroup( 'CAU', '#00FFFF'),
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160 ColorGroup( 'CAC', '#00FFFF'),
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161
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162 ColorGroup( 'AAA', '#00FFFF'),
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163 ColorGroup( 'AAG', '#00FFFF'),
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164
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165 ColorGroup( 'CGT', '#00FFFF'),
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166 ColorGroup( 'CGU', '#00FFFF'),
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167 ColorGroup( 'CGC', '#00FFFF'),
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168 ColorGroup( 'CGA', '#00FFFF'),
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169 ColorGroup( 'CGG', '#00FFFF'),
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170 ColorGroup( 'AGA', '#00FFFF'),
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171 ColorGroup( 'AGG', '#00FFFF'),
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172
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173
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174 ColorGroup( 'GAT', '#FF0000'),
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175 ColorGroup( 'GAU', '#FF0000'),
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176 ColorGroup( 'GAC', '#FF0000'),
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177
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178 ColorGroup( 'GAA', '#FF0000'),
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179 ColorGroup( 'GAG', '#FF0000'),
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180
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181
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182 ColorGroup( 'TCT', '#00FF00'),
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183 ColorGroup( 'UCU', '#00FF00'),
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184 ColorGroup( 'TCC', '#00FF00'),
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185 ColorGroup( 'UCC', '#00FF00'),
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186 ColorGroup( 'TCA', '#00FF00'),
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187 ColorGroup( 'UCA', '#00FF00'),
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188 ColorGroup( 'TCG', '#00FF00'),
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189 ColorGroup( 'UCG', '#00FF00'),
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190 ColorGroup( 'AGT', '#00FF00'),
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191 ColorGroup( 'AGU', '#00FF00'),
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192 ColorGroup( 'AGC', '#00FF00'),
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193
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194 ColorGroup( 'ACT', '#00FF00'),
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195 ColorGroup( 'ACU', '#00FF00'),
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196 ColorGroup( 'ACC', '#00FF00'),
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197 ColorGroup( 'ACA', '#00FF00'),
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198 ColorGroup( 'ACG', '#00FF00'),
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199
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200 ColorGroup( 'CAA', '#00FF00'),
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201 ColorGroup( 'CAG', '#00FF00'),
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202
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203 ColorGroup( 'AAT', '#00FF00'),
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204 ColorGroup( 'AAU', '#00FF00'),
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205 ColorGroup( 'AAC', '#00FF00'),
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206
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207
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208 ColorGroup( 'GCT', '#5555FF'),
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209 ColorGroup( 'GCU', '#5555FF'),
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210 ColorGroup( 'GCC', '#5555FF'),
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211 ColorGroup( 'GCA', '#5555FF'),
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212 ColorGroup( 'GCG', '#5555FF'),
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213
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214 ColorGroup( 'GTT', '#5555FF'),
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215 ColorGroup( 'GUU', '#5555FF'),
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216 ColorGroup( 'GTC', '#5555FF'),
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217 ColorGroup( 'GUC', '#5555FF'),
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218 ColorGroup( 'GTA', '#5555FF'),
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219 ColorGroup( 'GUA', '#5555FF'),
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220 ColorGroup( 'GTG', '#5555FF'),
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221 ColorGroup( 'GUG', '#5555FF'),
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222
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223 ColorGroup( 'CTT', '#5555FF'),
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224 ColorGroup( 'CUU', '#5555FF'),
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225 ColorGroup( 'CTC', '#5555FF'),
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226 ColorGroup( 'CUC', '#5555FF'),
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227 ColorGroup( 'CTA', '#5555FF'),
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228 ColorGroup( 'CUA', '#5555FF'),
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229 ColorGroup( 'CTG', '#5555FF'),
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230 ColorGroup( 'CUG', '#5555FF'),
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231 ColorGroup( 'TTA', '#5555FF'),
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232 ColorGroup( 'UUA', '#5555FF'),
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233 ColorGroup( 'TTG', '#5555FF'),
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234 ColorGroup( 'UUG', '#5555FF'),
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235
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236 ColorGroup( 'ATT', '#5555FF'),
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237 ColorGroup( 'AUU', '#5555FF'),
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238 ColorGroup( 'ATC', '#5555FF'),
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239 ColorGroup( 'AUC', '#5555FF'),
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240 ColorGroup( 'ATA', '#5555FF'),
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241 ColorGroup( 'AUA', '#5555FF'),
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242
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243 ColorGroup( 'ATG', '#5555FF'),
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244 ColorGroup( 'AUG', '#5555FF'),
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245
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246
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247 ColorGroup( 'TTT', '#FF00FF'),
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248 ColorGroup( 'UUU', '#FF00FF'),
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249 ColorGroup( 'TTC', '#FF00FF'),
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250 ColorGroup( 'UUC', '#FF00FF'),
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251
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252 ColorGroup( 'TAT', '#FF00FF'),
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253 ColorGroup( 'UAU', '#FF00FF'),
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254 ColorGroup( 'TAC', '#FF00FF'),
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255 ColorGroup( 'UAC', '#FF00FF'),
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256
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257 ColorGroup( 'TGG', '#FF00FF'),
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258 ColorGroup( 'UGG', '#FF00FF'),
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259
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260
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261 ColorGroup( 'GGT', '#996600'),
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262 ColorGroup( 'GGU', '#996600'),
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263 ColorGroup( 'GGC', '#996600'),
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264 ColorGroup( 'GGA', '#996600'),
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265 ColorGroup( 'GGG', '#996600'),
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266
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267 ColorGroup( 'CCT', '#996600'),
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268 ColorGroup( 'CCU', '#996600'),
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269 ColorGroup( 'CCC', '#996600'),
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270 ColorGroup( 'CCA', '#996600'),
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271 ColorGroup( 'CCG', '#996600'),
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272
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273
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274 ColorGroup( 'TGT', '#FFFF00'),
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275 ColorGroup( 'UGU', '#FFFF00'),
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276 ColorGroup( 'TGC', '#FFFF00'),
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277 ColorGroup( 'UGC', '#FFFF00'),
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278
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279 ColorGroup( 'TAA', '#000000'),
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280 ColorGroup( 'UAA', '#000000'),
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281 ColorGroup( 'TAG', '#000000'),
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282 ColorGroup( 'UAG', '#000000'),
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283 ColorGroup( 'TGA', '#000000'),
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284 ColorGroup( 'UGA', '#000000')],
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285 alphabet = codon_alphabetU
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286 )
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287 codonsT = ColorScheme([
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288 ColorGroup( 'CAT', '#00FFFF'),
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289 ColorGroup( 'CAU', '#00FFFF'),
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290 ColorGroup( 'CAC', '#00FFFF'),
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291
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292 ColorGroup( 'AAA', '#00FFFF'),
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293 ColorGroup( 'AAG', '#00FFFF'),
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294
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295 ColorGroup( 'CGT', '#00FFFF'),
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296 ColorGroup( 'CGU', '#00FFFF'),
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297 ColorGroup( 'CGC', '#00FFFF'),
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298 ColorGroup( 'CGA', '#00FFFF'),
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299 ColorGroup( 'CGG', '#00FFFF'),
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300 ColorGroup( 'AGA', '#00FFFF'),
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301 ColorGroup( 'AGG', '#00FFFF'),
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302
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303
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304 ColorGroup( 'GAT', '#FF0000'),
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305 ColorGroup( 'GAU', '#FF0000'),
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306 ColorGroup( 'GAC', '#FF0000'),
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307
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308 ColorGroup( 'GAA', '#FF0000'),
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309 ColorGroup( 'GAG', '#FF0000'),
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310
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311
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312 ColorGroup( 'TCT', '#00FF00'),
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313 ColorGroup( 'UCU', '#00FF00'),
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314 ColorGroup( 'TCC', '#00FF00'),
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315 ColorGroup( 'UCC', '#00FF00'),
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316 ColorGroup( 'TCA', '#00FF00'),
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317 ColorGroup( 'UCA', '#00FF00'),
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318 ColorGroup( 'TCG', '#00FF00'),
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319 ColorGroup( 'UCG', '#00FF00'),
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320 ColorGroup( 'AGT', '#00FF00'),
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321 ColorGroup( 'AGU', '#00FF00'),
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322 ColorGroup( 'AGC', '#00FF00'),
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323
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324 ColorGroup( 'ACT', '#00FF00'),
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325 ColorGroup( 'ACU', '#00FF00'),
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326 ColorGroup( 'ACC', '#00FF00'),
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327 ColorGroup( 'ACA', '#00FF00'),
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328 ColorGroup( 'ACG', '#00FF00'),
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329
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330 ColorGroup( 'CAA', '#00FF00'),
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331 ColorGroup( 'CAG', '#00FF00'),
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332
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333 ColorGroup( 'AAT', '#00FF00'),
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334 ColorGroup( 'AAU', '#00FF00'),
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335 ColorGroup( 'AAC', '#00FF00'),
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336
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337
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338 ColorGroup( 'GCT', '#5555FF'),
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339 ColorGroup( 'GCU', '#5555FF'),
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340 ColorGroup( 'GCC', '#5555FF'),
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341 ColorGroup( 'GCA', '#5555FF'),
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342 ColorGroup( 'GCG', '#5555FF'),
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343
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344 ColorGroup( 'GTT', '#5555FF'),
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345 ColorGroup( 'GUU', '#5555FF'),
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346 ColorGroup( 'GTC', '#5555FF'),
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347 ColorGroup( 'GUC', '#5555FF'),
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348 ColorGroup( 'GTA', '#5555FF'),
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349 ColorGroup( 'GUA', '#5555FF'),
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350 ColorGroup( 'GTG', '#5555FF'),
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351 ColorGroup( 'GUG', '#5555FF'),
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352
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353 ColorGroup( 'CTT', '#5555FF'),
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354 ColorGroup( 'CUU', '#5555FF'),
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355 ColorGroup( 'CTC', '#5555FF'),
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356 ColorGroup( 'CUC', '#5555FF'),
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357 ColorGroup( 'CTA', '#5555FF'),
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358 ColorGroup( 'CUA', '#5555FF'),
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359 ColorGroup( 'CTG', '#5555FF'),
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360 ColorGroup( 'CUG', '#5555FF'),
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361 ColorGroup( 'TTA', '#5555FF'),
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362 ColorGroup( 'UUA', '#5555FF'),
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363 ColorGroup( 'TTG', '#5555FF'),
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364 ColorGroup( 'UUG', '#5555FF'),
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365
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366 ColorGroup( 'ATT', '#5555FF'),
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367 ColorGroup( 'AUU', '#5555FF'),
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368 ColorGroup( 'ATC', '#5555FF'),
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369 ColorGroup( 'AUC', '#5555FF'),
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370 ColorGroup( 'ATA', '#5555FF'),
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371 ColorGroup( 'AUA', '#5555FF'),
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372
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373 ColorGroup( 'ATG', '#5555FF'),
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374 ColorGroup( 'AUG', '#5555FF'),
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375
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376
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377 ColorGroup( 'TTT', '#FF00FF'),
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378 ColorGroup( 'UUU', '#FF00FF'),
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379 ColorGroup( 'TTC', '#FF00FF'),
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380 ColorGroup( 'UUC', '#FF00FF'),
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381
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382 ColorGroup( 'TAT', '#FF00FF'),
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383 ColorGroup( 'UAU', '#FF00FF'),
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384 ColorGroup( 'TAC', '#FF00FF'),
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385 ColorGroup( 'UAC', '#FF00FF'),
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386
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387 ColorGroup( 'TGG', '#FF00FF'),
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388 ColorGroup( 'UGG', '#FF00FF'),
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389
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390
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391 ColorGroup( 'GGT', '#996600'),
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392 ColorGroup( 'GGU', '#996600'),
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393 ColorGroup( 'GGC', '#996600'),
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394 ColorGroup( 'GGA', '#996600'),
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395 ColorGroup( 'GGG', '#996600'),
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396
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397 ColorGroup( 'CCT', '#996600'),
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398 ColorGroup( 'CCU', '#996600'),
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399 ColorGroup( 'CCC', '#996600'),
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400 ColorGroup( 'CCA', '#996600'),
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401 ColorGroup( 'CCG', '#996600'),
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402
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403
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404 ColorGroup( 'TGT', '#FFFF00'),
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405 ColorGroup( 'UGU', '#FFFF00'),
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406 ColorGroup( 'TGC', '#FFFF00'),
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407 ColorGroup( 'UGC', '#FFFF00'),
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408
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409 ColorGroup( 'TAA', '#000000'),
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410 ColorGroup( 'UAA', '#000000'),
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411 ColorGroup( 'TAG', '#000000'),
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412 ColorGroup( 'UAG', '#000000'),
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413 ColorGroup( 'TGA', '#000000'),
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414 ColorGroup( 'UGA', '#000000')],
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415 alphabet = codon_alphabetT
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|
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416 )
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417
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418
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419
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420
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421 charge = ColorScheme([
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422 ColorGroup("KRH", "blue", "Positive" ),
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423 ColorGroup( "DE", "red", "Negative") ],
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424 alphabet = seq.unambiguous_protein_alphabet
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|
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425 )
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426
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427
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428 taylor = ColorScheme([
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429 ColorGroup( 'A', '#CCFF00' ),
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430 ColorGroup( 'C', '#FFFF00' ),
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431 ColorGroup( 'D', '#FF0000'),
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432 ColorGroup( 'E', '#FF0066' ),
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433 ColorGroup( 'F', '#00FF66'),
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434 ColorGroup( 'G', '#FF9900'),
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435 ColorGroup( 'H', '#0066FF'),
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436 ColorGroup( 'I', '#66FF00'),
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437 ColorGroup( 'K', '#6600FF'),
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438 ColorGroup( 'L', '#33FF00'),
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439 ColorGroup( 'M', '#00FF00'),
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440 ColorGroup( 'N', '#CC00FF'),
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441 ColorGroup( 'P', '#FFCC00'),
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442 ColorGroup( 'Q', '#FF00CC'),
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443 ColorGroup( 'R', '#0000FF'),
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444 ColorGroup( 'S', '#FF3300'),
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445 ColorGroup( 'T', '#FF6600'),
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446 ColorGroup( 'V', '#99FF00'),
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447 ColorGroup( 'W', '#00CCFF'),
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448 ColorGroup( 'Y', '#00FFCC')],
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449 title = "Taylor",
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|
450 description = "W. Taylor, Protein Engineering, Vol 10 , 743-746 (1997)",
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|
|
451 alphabet = seq.unambiguous_protein_alphabet
|
|
|
452 )
|
|
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453
|
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454
|
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455
|
