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1 ggcwin
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2 Function
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3
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4 Calculates the GC content along the given genome
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5
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6 Description
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7
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8 ggcwin calculates and plots the GC content of the given sequence.
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9
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10 G-language SOAP service is provided by the
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11 Institute for Advanced Biosciences, Keio University.
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12 The original web service is located at the following URL:
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13
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14 http://www.g-language.org/wiki/soap
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15
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16 WSDL(RPC/Encoded) file is located at:
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17
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18 http://soap.g-language.org/g-language.wsdl
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19
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20 Documentation on G-language Genome Analysis Environment methods are
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21 provided at the Document Center
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22
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23 http://ws.g-language.org/gdoc/
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24
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25 Usage
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26
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27 Here is a sample session with ggcwin
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28
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29 % ggcwin refseqn:NC_000913
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30 Calculates the GC content along the given genome
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31 Program compseq output file (optional) [nc_000913.ggcwin]:
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32
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33 Go to the input files for this example
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34 Go to the output files for this example
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35
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36 Example 2
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37
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38 % ggcwin refseqn:NC_000913 -plot -graph png
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39 Calculates the GC content along the given genome
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40 Created ggcwin.1.png
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41
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42 Go to the input files for this example
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43 Go to the output files for this example
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44
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45 Command line arguments
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46
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47 Standard (Mandatory) qualifiers (* if not always prompted):
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48 [-sequence] seqall Nucleotide sequence(s) filename and optional
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49 format, or reference (input USA)
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50 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
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51 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
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52 tek, tekt, none, data, xterm, png, gif, svg)
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53 * -outfile outfile [*.ggcwin] Program compseq output file
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54 (optional)
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55
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56 Additional (Optional) qualifiers: (none)
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57 Advanced (Unprompted) qualifiers:
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58 -window integer [10000] Window size to observe (Any integer
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59 value)
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60 -at boolean [N] Include for observing AT skew instead of
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61 GC skew
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62 -purine boolean [N] Include for observing purine (AG/TC)
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63 skew
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64 -keto boolean [N] Include for observing keto (TG/AC) skew
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65 default: "0
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66 -plot toggle [N] Include to plot result
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67
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68 Associated qualifiers:
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69
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70 "-sequence" associated qualifiers
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71 -sbegin1 integer Start of each sequence to be used
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72 -send1 integer End of each sequence to be used
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73 -sreverse1 boolean Reverse (if DNA)
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74 -sask1 boolean Ask for begin/end/reverse
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75 -snucleotide1 boolean Sequence is nucleotide
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76 -sprotein1 boolean Sequence is protein
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77 -slower1 boolean Make lower case
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78 -supper1 boolean Make upper case
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79 -scircular1 boolean Sequence is circular
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80 -sformat1 string Input sequence format
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81 -iquery1 string Input query fields or ID list
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82 -ioffset1 integer Input start position offset
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83 -sdbname1 string Database name
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84 -sid1 string Entryname
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85 -ufo1 string UFO features
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86 -fformat1 string Features format
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87 -fopenfile1 string Features file name
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88
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89 "-graph" associated qualifiers
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90 -gprompt boolean Graph prompting
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91 -gdesc string Graph description
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92 -gtitle string Graph title
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93 -gsubtitle string Graph subtitle
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94 -gxtitle string Graph x axis title
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95 -gytitle string Graph y axis title
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96 -goutfile string Output file for non interactive displays
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97 -gdirectory string Output directory
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98
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99 "-outfile" associated qualifiers
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100 -odirectory string Output directory
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101
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102 General qualifiers:
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103 -auto boolean Turn off prompts
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104 -stdout boolean Write first file to standard output
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105 -filter boolean Read first file from standard input, write
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106 first file to standard output
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107 -options boolean Prompt for standard and additional values
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108 -debug boolean Write debug output to program.dbg
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109 -verbose boolean Report some/full command line options
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110 -help boolean Report command line options and exit. More
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111 information on associated and general
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112 qualifiers can be found with -help -verbose
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113 -warning boolean Report warnings
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114 -error boolean Report errors
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115 -fatal boolean Report fatal errors
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116 -die boolean Report dying program messages
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117 -version boolean Report version number and exit
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118
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119 Input file format
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120
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121 The database definitions for following commands are available at
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122 http://soap.g-language.org/kbws/embossrc
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123
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124 ggcwin reads one or more nucleotide sequences.
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125
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126 Output file format
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127
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128 The output from ggcwin is to a plain text file or the EMBOSS graphics device.
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129
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130 File: nc_000913.ggcwin
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131
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132 Sequence: NC_000913
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133 location,GC content
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134 0,0.520700
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135 10000,0.499400
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136 20000,0.526200
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137 30000,0.532300
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138 40000,0.527700
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139 50000,0.515600
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140 60000,0.555800
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141 70000,0.536000
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142
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143 [Part of this file has been deleted for brevity]
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144
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145 4530000,0.442800
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146 4540000,0.487000
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147 4550000,0.507700
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148 4560000,0.509600
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149 4570000,0.444600
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150 4580000,0.531600
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151 4590000,0.512300
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152 4600000,0.504500
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153 4610000,0.535600
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154 4620000,0.546600
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155
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156
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157 Data files
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158
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159 None.
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160
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161 Notes
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162
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163 None.
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164
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165 References
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166
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167 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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168 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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169 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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170
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171 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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172 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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173 31, 7.
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174
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175 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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176 Analysis Environment with REST and SOAP Web Service Interfaces,
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177 Nucleic Acids Res., 38, W700-W705.
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178
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179 Warnings
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180
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181 None.
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182
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183 Diagnostic Error Messages
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184
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185 None.
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186
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187 Exit status
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188
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189 It always exits with a status of 0.
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190
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191 Known bugs
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192
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193 None.
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194
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195 See also
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196
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197 ggcskew Calculates the GC skew of the input sequence
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198 ggeneskew Calculate the gene strand bias of the given genome
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199 ggenomicskew Calculates the GC skew in different regions of the given genom
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200
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201 Author(s)
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202
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203 Hidetoshi Itaya (celery@g-language.org)
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204 Institute for Advanced Biosciences, Keio University
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205 252-0882 Japan
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206
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207 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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208 Institute for Advanced Biosciences, Keio University
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209 252-0882 Japan
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210
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211 History
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212
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213 2012 - Written by Hidetoshi Itaya
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214 2013 - Fixed by Hidetoshi Itaya
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215
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216 Target users
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217
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218 This program is intended to be used by everyone and everything, from
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219 naive users to embedded scripts.
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220
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221 Comments
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222
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223 None.
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224
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