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1 ggenomemap3
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2 Function
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3
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4 Draws the map of the genome (version 3)
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5
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6 Description
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7
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8 ggenomemap3 creates a map of the genome, showing the local nucleotide
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9 contents and positions of genes. A is shown in red, T is shown in green,
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10 G is shown in yellow, and C is shown in blue.
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11 Created image has a resolution of 8192x8192 and is suited for conversion
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12 to SVG, which can be performed by specifying the -format option. The formats
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13 available are dependent to the "convert" command from ImageMagick.
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14
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15 G-language SOAP service is provided by the
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16 Institute for Advanced Biosciences, Keio University.
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17 The original web service is located at the following URL:
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18
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19 http://www.g-language.org/wiki/soap
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20
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21 WSDL(RPC/Encoded) file is located at:
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22
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23 http://soap.g-language.org/g-language.wsdl
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24
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25 Documentation on G-language Genome Analysis Environment methods are
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26 provided at the Document Center
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27
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28 http://ws.g-language.org/gdoc/
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29
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30 Usage
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31
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32 Here is a sample session with ggenomemap3
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33
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34 % ggenomemap3 refseqn:NC_000913
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35 Draws the map of the genome (version 3)
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36 Created ggenomemap3.1.png
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37
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38 Go to the input files for this example
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39 Go to the output files for this example
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40
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41 Command line arguments
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42
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43 Standard (Mandatory) qualifiers:
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44 [-sequence] seqall Nucleotide sequence(s) filename and optional
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45 format, or reference (input USA)
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46
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47 Additional (Optional) qualifiers: (none)
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48 Advanced (Unprompted) qualifiers:
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49 -format string [png] Output file format. Dependent on
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50 'convert' command (Any string)
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51 -width integer [8192] Image width (Any integer value)
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52 -height integer [8192] Image height (Any integer value)
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53 -[no]accid boolean [Y] Include to use sequence accession ID as
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54 query
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55 -goutfile string [ggenomemap3] Output file for non
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56 interactive displays (Any string)
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57
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58 Associated qualifiers:
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59
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60 "-sequence" associated qualifiers
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61 -sbegin1 integer Start of each sequence to be used
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62 -send1 integer End of each sequence to be used
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63 -sreverse1 boolean Reverse (if DNA)
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64 -sask1 boolean Ask for begin/end/reverse
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65 -snucleotide1 boolean Sequence is nucleotide
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66 -sprotein1 boolean Sequence is protein
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67 -slower1 boolean Make lower case
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68 -supper1 boolean Make upper case
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69 -scircular1 boolean Sequence is circular
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70 -sformat1 string Input sequence format
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71 -iquery1 string Input query fields or ID list
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72 -ioffset1 integer Input start position offset
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73 -sdbname1 string Database name
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74 -sid1 string Entryname
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75 -ufo1 string UFO features
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76 -fformat1 string Features format
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77 -fopenfile1 string Features file name
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78
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79 General qualifiers:
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80 -auto boolean Turn off prompts
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81 -stdout boolean Write first file to standard output
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82 -filter boolean Read first file from standard input, write
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83 first file to standard output
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84 -options boolean Prompt for standard and additional values
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85 -debug boolean Write debug output to program.dbg
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86 -verbose boolean Report some/full command line options
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87 -help boolean Report command line options and exit. More
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88 information on associated and general
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89 qualifiers can be found with -help -verbose
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90 -warning boolean Report warnings
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91 -error boolean Report errors
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92 -fatal boolean Report fatal errors
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93 -die boolean Report dying program messages
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94 -version boolean Report version number and exit
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95
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96 Input file format
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97
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98 The database definitions for following commands are available at
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99 http://soap.g-language.org/kbws/embossrc
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100
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101 ggenomemap3 reads one or more nucleotide sequences.
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102
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103 Output file format
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104
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105 The output from ggenomemap3 is to an image file.
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106
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107 Data files
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108
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109 None.
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110
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111 Notes
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112
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113 None.
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114
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115 References
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116
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117 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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118 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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119 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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120
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121 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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122 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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123 31, 7.
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124
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125 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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126 Analysis Environment with REST and SOAP Web Service Interfaces,
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127 Nucleic Acids Res., 38, W700-W705.
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128
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129 Warnings
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130
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131 None.
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132
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133 Diagnostic Error Messages
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134
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135 None.
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136
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137 Exit status
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138
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139 It always exits with a status of 0.
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140
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141 Known bugs
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142
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143 None.
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144
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145 See also
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146
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147 gcircularmap Draws circular map of the genome
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148 gdnawalk Draws DNA Walk map of the genome
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149
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150 Author(s)
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151
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152 Hidetoshi Itaya (celery@g-language.org)
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153 Institute for Advanced Biosciences, Keio University
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154 252-0882 Japan
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155
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156 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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157 Institute for Advanced Biosciences, Keio University
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158 252-0882 Japan
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159
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160 History
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161
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162 2012 - Written by Hidetoshi Itaya
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163 2013 - Fixed by Hidetoshi Itaya
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164
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165 Target users
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166
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167 This program is intended to be used by everyone and everything, from
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168 naive users to embedded scripts.
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169
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170 Comments
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171
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172 None.
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173
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