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1 NAME
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2 InfoNucleicAcids.pl - List properties of nucleic acids
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3
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4 SYNOPSIS
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5 InfoNucleicAcids.pl NucleicAcidIDs...
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6
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7 InfoNucleicAcids.pl [-h, --help] [-m, --mode NucleicAcidID |
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8 NucleicAcidType] [--OutDelim comma | tab | semicolon] [--output STDOUT |
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9 File] [--OutputStyle NucleicAcidBlock | NucleicAcidRows] [-o,
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10 --overwrite] [--precision number] [--PropertiesMode Categories | Names |
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11 All] [-p, --properties CategoryName, [CategoryName,...] | PropertyName,
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12 [PropertyName,...]] [--PropertiesListing ByGroup | Alphabetical] [-q,
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13 --quote yes | no] [-r, --root rootname] [-w, --WorkingDir dirname]
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14 NucleicAcidIDs...
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15
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16 DESCRIPTION
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17 List nucleic acid properties. Nucleic acids identification supports two
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18 types of IDs: code or name. Nucleic acid properties data, in addition to
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19 basic information about nucleic acids - code, name, type, chemical
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20 formula and molecular weight - include information about exact mass and
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21 elemental composition.
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22
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23 PARAMETERS
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24 NucleicAcidIDs *Code [NucleicAcidName...] | NucleicAcidType
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25 [NucleicAcidType...]*
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26 *NucleicAcidIDs* is a space delimited list of values to identify
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27 nucleic acids.
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28
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29 For *NucleicAcidID* mode, input value format is: *Code
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30 [NucleicAcidName...]*. Default: *A*. Examples:
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31
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32 A
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33 dG AMP
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34 Cytidine T UDP dpppA "5'-dATP"
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35
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36 For *NucleicAcidType* mode, input value format is: *NucleicAcidType
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37 [NucleicAcidType...]*. Default: *A*. Possible values are:
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38 *Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide,
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39 Deoxynucleotide*. Default: *Nucleoside*. Examples:
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40
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41 Deoxynucleoside
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42 Nucleobase Nucleotide
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43
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44 OPTIONS
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45 -h, --help
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46 Print this help message.
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47
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48 -m, --mode *NucleicAcidID | NucleicAcidType*
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49 Specify nucleic acids for listing properties using one of these
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50 methods: nucleic acid code and/or names or nucleic acid type.
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51
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52 Possible values: *NucleicAcidID or NucleicAcidType*. Default:
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53 *NucleicAcidID*
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54
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55 For *NucleicAcidType*, command line parameters support these type:
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56 *Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide,
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57 Deoxynucleotide*.
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58
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59 --OutDelim *comma | tab | semicolon*
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60 Output text file delimiter. Possible values: *comma, tab, or
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61 semicolon* Default value: *comma*.
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62
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63 --output *STDOUT | File*
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64 List information at STDOUT or write it to a file. Possible values:
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65 *STDOUT or File*. Default: *STDOUT*. -r, --root option is used to
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66 generate output file name.
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67
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68 --OutputStyle *NucleicAcidBlock | NucleicAcidRows*
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69 Specify how to list nucleic acid information: add a new line for
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70 each property and present it as a block for each nucleic acid; or
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71 include all properties in one line and show it as a single line.
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72
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73 Possible values: *NucleicAcidBlock | NucleicAcidRows*. Default:
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74 *NucleicAcidBlock*
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75
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76 An example for *NucleicAcidBlock* output style:
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77
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78 Code: Ado
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79 OtherCodes: A
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80 Name: Adenosine
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81 Type: Nucleoside
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82 MolecularFormula: C10H13O4N5
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83 MolecularWeight: 267.2413
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84 ... ...
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85
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86 An example for *NucleicAcidRows* output style:
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87
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88 Code,OtherCodes,Name,Type,MolecularFormula,MolecularWeight
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89
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90 -o, --overwrite
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91 Overwrite existing files.
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92
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93 --precision *number*
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94 Precision for listing numerical values. Default: up to *4* decimal
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95 places. Valid values: positive integers.
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96
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97 --PropertiesMode *Categories | Names | All*
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98 Specify how property names are specified: use category names;
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99 explicit list of property names; or use all available properties.
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100 Possible values: *Categories, Names, or All*. Default: *Categories*.
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101
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102 This option is used in conjunction with -p, --properties option to
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103 specify properties of interest.
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104
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105 -p, --properties *CategoryName,[CategoryName,...] |
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106 PropertyName,[PropertyName,...]*
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107 This option is --propertiesmode specific. In general, it's a list of
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108 comma separated category or property names.
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109
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110 Specify which nucleic acid properties information to list for the
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111 nucleic acid IDs specified using command line parameters: list basic
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112 information; list all available information; or specify a comma
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113 separated list of nucleic acid property names.
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114
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115 Possible values: *Basic | BasicPlus |
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116 PropertyName,[PropertyName,...]*. Default: *Basic*.
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117
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118 *Basic* includes: *Code, OtherCodes, Name, Type, MolecularFormula,
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119 MolecularWeight*
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120
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121 *BasicPlus* includes: *Code, OtherCodes, Name, Type,
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122 MolecularFormula, MolecularWeight, ExactMass, ElementalComposition*
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123
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124 Here is a complete list of available properties: *Code, OtherCodes,
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125 BasePair, Name, Type, MolecularFormula, MolecularFormulaAtpH7.5,
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126 MolecularWeight, ExactMass, ElementalComposition*.
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127
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128 --PropertiesListing *ByGroup | Alphabetical*
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129 Specify how to list properties for nucleic acids: group by category
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130 or an alphabetical by property names. Possible values: *ByGroup or
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131 Alphabetical*. Default: *ByGroup*
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132
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133 -q, --quote *yes | no*
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134 Put quotes around column values in output text file. Possible
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135 values: *yes or no*. Default value: *yes*.
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136
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137 -r, --root *rootname*
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138 New text file name is generated using the root: <Root>.<Ext>. File
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139 name is only used during *File* value of -o, --output option.
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140
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141 Default file name: NucleicAcidInfo<mode>.<Ext>. The csv, and tsv
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142 <Ext> values are used for comma/semicolon, and tab delimited text
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143 files respectively.
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144
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145 -w, --WorkingDir *dirname*
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146 Location of working directory. Default: current directory.
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147
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148 EXAMPLES
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149 To list basic properties information for nucleoside A, type:
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150
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151 % InfoNucleicAcids.pl
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152
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153 To list all available properties information for nucleoside A, type:
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154
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155 % InfoNucleicAcids.pl --propertiesmode all A
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156
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157 To list all available information for all available nucleic acids, type:
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158
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159 % InfoNucleicAcids.pl --propertiesmode All All
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160
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161 To list basic properties information for all nucleobases, type:
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162
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163 % InfoNucleicAcids.pl -m NucleicAcidType Nucleoside
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164
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165 To list basic properties information for all nucleotides and
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166 deoxynulceotides, type:
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167
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168 % InfoNucleicAcids.pl -m NucleicAcidType Nucleotide Deoxynucleotide
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169
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170 To list basic properties information for variety of nucleic acids, type:
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171
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172 % InfoNucleicAcids.pl A dG AMP Cytidine T UDP "5'-dATP"
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173
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174 To list code and molecular weights for nucleosides A, G, C and T, type:
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175
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176 % InfoNucleicAcids.pl --PropertiesMode Names --properties
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177 Code,MolecularWeight A G C T
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178
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179 To alphabetically list all the available properties for nucleotides
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180 dAMP, dGMP, dCMP, and dTMP in rows instead of nucleic acid blocks with
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181 quotes around the values, type:
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182
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183 % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing
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184 Alphabetical --OutputStyle NucleicAcidRows -q yes dAMP dGMP
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185 dCMP dTMP
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186
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187 To alphabetically list all the available properties for all available
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188 nucleic acids to a file names NucleicAcidsProperties.csv with quotes
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189 around the values, type
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190
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191 % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing
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192 Alphabetical --output File --OutputStyle NucleicAcidRows -r
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193 NucleicAcidsProperties -o -q Yes All
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194
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195 AUTHOR
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196 Manish Sud <msud@san.rr.com>
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197
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198 SEE ALSO
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199 InfoAminoAcids.pl, InfoPeriodicTableElements.pl
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200
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201 COPYRIGHT
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202 Copyright (C) 2015 Manish Sud. All rights reserved.
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203
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204 This file is part of MayaChemTools.
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205
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206 MayaChemTools is free software; you can redistribute it and/or modify it
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207 under the terms of the GNU Lesser General Public License as published by
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208 the Free Software Foundation; either version 3 of the License, or (at
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209 your option) any later version.
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210
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