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1 gcircularmap
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2 Function
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3
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4 Draws circular map of the genome
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5
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6 Description
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7
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8 gdnawalk creates a circular map of the genome using SVG, suitable for
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9 plasmids and circular bacterial chromosomes.
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10
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11 From the outer ring inwards, genes on direct strand (pink),
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12 genes on complementary strand (yellow), tRNAs (green arrows),
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13 rRNAs (pink or orange stripes depending on the strand),
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14 GC content (brown lines), GC skew (yellow lines). Replication
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15 origin and terminus predicted from the GC skew shift points
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16 are also labeled.
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17
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18 G-language SOAP service is provided by the
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19 Institute for Advanced Biosciences, Keio University.
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20 The original web service is located at the following URL:
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21
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22 http://www.g-language.org/wiki/soap
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23
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24 WSDL(RPC/Encoded) file is located at:
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25
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26 http://soap.g-language.org/g-language.wsdl
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27
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28 Documentation on G-language Genome Analysis Environment methods are
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29 provided at the Document Center
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30
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31 http://ws.g-language.org/gdoc/
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32
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33 Usage
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34
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35 Here is a sample session with gcircularmap
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36
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37 % gcircularmap refseqn:NC_000913
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38 Draws circular map of the genome
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39 Created gcircularmap.1.svg
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40
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41 Go to the input files for this example
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42 Go to the output files for this example
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43
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44 Command line arguments
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45
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46 Standard (Mandatory) qualifiers:
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47 [-sequence] seqall Nucleotide sequence(s) filename and optional
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48 format, or reference (input USA)
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49
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50 Additional (Optional) qualifiers: (none)
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51 Advanced (Unprompted) qualifiers:
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52 -format string [svg] Output file format. Dependent on
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53 'convert' command (Any string)
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54 -[no]accid boolean [Y] Include to use sequence accession ID as
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55 query
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56 -goutfile string [gcircularmap] Output file for non
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57 interactive displays (Any string)
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58
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59 Associated qualifiers:
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60
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61 "-sequence" associated qualifiers
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62 -sbegin1 integer Start of each sequence to be used
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63 -send1 integer End of each sequence to be used
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64 -sreverse1 boolean Reverse (if DNA)
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65 -sask1 boolean Ask for begin/end/reverse
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66 -snucleotide1 boolean Sequence is nucleotide
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67 -sprotein1 boolean Sequence is protein
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68 -slower1 boolean Make lower case
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69 -supper1 boolean Make upper case
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70 -scircular1 boolean Sequence is circular
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71 -sformat1 string Input sequence format
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72 -iquery1 string Input query fields or ID list
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73 -ioffset1 integer Input start position offset
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74 -sdbname1 string Database name
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75 -sid1 string Entryname
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76 -ufo1 string UFO features
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77 -fformat1 string Features format
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78 -fopenfile1 string Features file name
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79
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80 General qualifiers:
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81 -auto boolean Turn off prompts
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82 -stdout boolean Write first file to standard output
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83 -filter boolean Read first file from standard input, write
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84 first file to standard output
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85 -options boolean Prompt for standard and additional values
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86 -debug boolean Write debug output to program.dbg
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87 -verbose boolean Report some/full command line options
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88 -help boolean Report command line options and exit. More
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89 information on associated and general
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90 qualifiers can be found with -help -verbose
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91 -warning boolean Report warnings
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92 -error boolean Report errors
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93 -fatal boolean Report fatal errors
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94 -die boolean Report dying program messages
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95 -version boolean Report version number and exit
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96
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97 Input file format
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98
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99 The database definitions for following commands are available at
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100 http://soap.g-language.org/kbws/embossrc
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101
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102 gcircularmap reads one or more nucleotide sequences.
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103
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104 Output file format
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105
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106 The output from gcircularmap is to an image file.
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107
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108 Data files
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109
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110 None.
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111
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112 Notes
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113
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114 None.
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115
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116 References
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117
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118 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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119 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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120 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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121
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122 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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123 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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124 31, 7.
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125
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126 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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127 Analysis Environment with REST and SOAP Web Service Interfaces,
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128 Nucleic Acids Res., 38, W700-W705.
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129
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130 Warnings
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131
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132 None.
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133
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134 Diagnostic Error Messages
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135
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136 None.
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137
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138 Exit status
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139
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140 It always exits with a status of 0.
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141
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142 Known bugs
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143
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144 None.
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145
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146 See also
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147
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148 gdnawalk Draws DNA Walk map of the genome
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149 ggenomemap3 Draws the map of the genome (version 3)
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150
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151 Author(s)
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152
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153 Hidetoshi Itaya (celery@g-language.org)
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154 Institute for Advanced Biosciences, Keio University
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155 252-0882 Japan
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156
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157 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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158 Institute for Advanced Biosciences, Keio University
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159 252-0882 Japan
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160
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161 History
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162
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163 2012 - Written by Hidetoshi Itaya
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164 2013 - Fixed by Hidetoshi Itaya
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165
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166 Target users
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167
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168 This program is intended to be used by everyone and everything, from
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169 naive users to embedded scripts.
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170
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171 Comments
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172
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173 None.
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174
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