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1 gcgr
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2 Function
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3
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4 Create a Chaos Game Representation of a given sequence
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5
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6 Description
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7
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8 gcgr creates a Chaos Game Representation (CGR) image of a given sequence.
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9 CGR is generated by the following procedure:
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10
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11 1. Start from position (0,0) or the origin of two dimensional coordinate.
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12 Four nucleotides are located at the four corners:
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13 A: (-1, 1) upper left
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14 T: (1, -1) lower right
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15 G: (1, 1) upper right
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16 C: (-1, -1) lower left
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17 2. For each nucleotide, move and mark the new location which is halfway
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18 between the current location and the nucleotide.
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19 For example, if the first letter is A, position is moved from (0,0) to
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20 midpoint between (-1, 1) and (0,0), which is (-0.5, 0.5).
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21
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22 3. Repeat this procedure for all nucleotides.
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23 CGR is a generalized scale-independent Markov probability table for the
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24 sequence, and oligomer tables can be deduced from CGR image.
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25
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26 G-language SOAP service is provided by the
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27 Institute for Advanced Biosciences, Keio University.
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28 The original web service is located at the following URL:
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29
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30 http://www.g-language.org/wiki/soap
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31
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32 WSDL(RPC/Encoded) file is located at:
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33
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34 http://soap.g-language.org/g-language.wsdl
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35
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36 Documentation on G-language Genome Analysis Environment methods are
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37 provided at the Document Center
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38
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39 http://ws.g-language.org/gdoc/
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40
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41 Usage
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42
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43 Here is a sample session with gcgr
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44
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45 % gcgr refseqn:NC_000913
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46 Create a Chaos Game Representation of a given sequence
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47 Created gcgr.1.png
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48
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49 Go to the input files for this example
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50 Go to the output files for this example
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51
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52 Command line arguments
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53
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54 Standard (Mandatory) qualifiers:
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55 [-sequence] seqall Nucleotide sequence(s) filename and optional
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56 format, or reference (input USA)
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57
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58 Additional (Optional) qualifiers: (none)
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59 Advanced (Unprompted) qualifiers:
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60 -format string [png] Output file format. Dependent on
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61 'convert' command (Any string)
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62 -width integer [1024] Width of image (Any integer value)
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63 -goutfile string [gcgr] Output file for non interactive
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64 displays (Any string)
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65
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66 Associated qualifiers:
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67
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68 "-sequence" associated qualifiers
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69 -sbegin1 integer Start of each sequence to be used
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70 -send1 integer End of each sequence to be used
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71 -sreverse1 boolean Reverse (if DNA)
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72 -sask1 boolean Ask for begin/end/reverse
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73 -snucleotide1 boolean Sequence is nucleotide
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74 -sprotein1 boolean Sequence is protein
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75 -slower1 boolean Make lower case
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76 -supper1 boolean Make upper case
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77 -scircular1 boolean Sequence is circular
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78 -sformat1 string Input sequence format
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79 -iquery1 string Input query fields or ID list
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80 -ioffset1 integer Input start position offset
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81 -sdbname1 string Database name
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82 -sid1 string Entryname
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83 -ufo1 string UFO features
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84 -fformat1 string Features format
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85 -fopenfile1 string Features file name
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86
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87 General qualifiers:
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88 -auto boolean Turn off prompts
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89 -stdout boolean Write first file to standard output
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90 -filter boolean Read first file from standard input, write
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91 first file to standard output
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92 -options boolean Prompt for standard and additional values
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93 -debug boolean Write debug output to program.dbg
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94 -verbose boolean Report some/full command line options
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95 -help boolean Report command line options and exit. More
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96 information on associated and general
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97 qualifiers can be found with -help -verbose
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98 -warning boolean Report warnings
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99 -error boolean Report errors
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100 -fatal boolean Report fatal errors
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101 -die boolean Report dying program messages
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102 -version boolean Report version number and exit
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103
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104 Input file format
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105
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106 The database definitions for following commands are available at
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107 http://soap.g-language.org/kbws/embossrc
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108
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109 gcgr reads one or more nucleotide sequences.
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110
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111 Output file format
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112
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113 The output from gcgr is to an image file.
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114
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115 Data files
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116
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117 None.
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118
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119 Notes
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120
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121 None.
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122
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123 References
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124
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125 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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126 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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127 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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128
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129 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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130 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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131 31, 7.
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132
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133 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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134 Analysis Environment with REST and SOAP Web Service Interfaces,
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135 Nucleic Acids Res., 38, W700-W705.
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136
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137 Warnings
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138
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139 None.
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140
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141 Diagnostic Error Messages
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142
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143 None.
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144
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145 Exit status
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146
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147 It always exits with a status of 0.
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148
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149 Known bugs
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150
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151 None.
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152
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153 See also
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154
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155 gseq2png Converts a sequence to PNG image
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156
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157 Author(s)
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158
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159 Hidetoshi Itaya (celery@g-language.org)
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160 Institute for Advanced Biosciences, Keio University
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161 252-0882 Japan
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162
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163 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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164 Institute for Advanced Biosciences, Keio University
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165 252-0882 Japan
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166
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167 History
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168
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169 2012 - Written by Hidetoshi Itaya
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170 2013 - Fixed by Hidetoshi Itaya
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171
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172 Target users
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173
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174 This program is intended to be used by everyone and everything, from
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175 naive users to embedded scripts.
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176
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177 Comments
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178
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179 None.
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180
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