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1 ggcskew
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2 Function
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3
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4 Calculates the GC skew of the input sequence
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5
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6 Description
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7
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8 ggcskew calculates and plots the GC skew of the given sequence. The "skew"
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9 of a sequence is calculated as (C-G)/(C+G) in GC skew. The program can
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10 alternatively calculate AT skew, purine skew, and keto skew, as well as
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11 cumulative skew. GC skew is used to observe various biological aspects
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12 such as prediction of replication origin and terminus in bacteria.
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13
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14 G-language SOAP service is provided by the
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15 Institute for Advanced Biosciences, Keio University.
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16 The original web service is located at the following URL:
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17
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18 http://www.g-language.org/wiki/soap
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19
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20 WSDL(RPC/Encoded) file is located at:
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21
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22 http://soap.g-language.org/g-language.wsdl
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23
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24 Documentation on G-language Genome Analysis Environment methods are
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25 provided at the Document Center
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26
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27 http://ws.g-language.org/gdoc/
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28
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29 Usage
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30
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31 Here is a sample session with ggcskew
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32
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33 % ggcskew refseqn:NC_000913
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34 Calculates the GC skew of the input sequence
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35 Program compseq output file (optional) [nc_000913.ggcskew]:
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36
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37 Go to the input files for this example
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38 Go to the output files for this example
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39
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40 Example 2
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41
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42 % ggcskew refseqn:NC_000913 -plot -graph png
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43 Calculates the GC skew of the input sequence
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44 Created ggcskew.1.png
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45
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46 Go to the input files for this example
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47 Go to the output files for this example
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48
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49 Command line arguments
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50
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51 Standard (Mandatory) qualifiers (* if not always prompted):
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52 [-sequence] seqall Nucleotide sequence(s) filename and optional
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53 format, or reference (input USA)
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54 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
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55 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
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56 tek, tekt, none, data, xterm, png, gif, svg)
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57 * -outfile outfile [*.ggcskew] Program compseq output file
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58 (optional)
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59
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60 Additional (Optional) qualifiers: (none)
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61 Advanced (Unprompted) qualifiers:
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62 -window integer [10000] Window size to observe (Any integer
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63 value)
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64 -slide integer [10000] Window slide size (Any integer
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65 value)
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66 -cumulative boolean [N] Include to calculate cumulative skew
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67 -at boolean [N] Include for observing AT skew instead of
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68 GC skew
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69 -purine boolean [N] Include for observing purine (AG/TC)
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70 skew
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71 -keto boolean [N] Include for observing keto (TG/AC) skew
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72 -plot toggle [N] Include to plot result
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73
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74 Associated qualifiers:
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75
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76 "-sequence" associated qualifiers
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77 -sbegin1 integer Start of each sequence to be used
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78 -send1 integer End of each sequence to be used
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79 -sreverse1 boolean Reverse (if DNA)
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80 -sask1 boolean Ask for begin/end/reverse
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81 -snucleotide1 boolean Sequence is nucleotide
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82 -sprotein1 boolean Sequence is protein
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83 -slower1 boolean Make lower case
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84 -supper1 boolean Make upper case
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85 -scircular1 boolean Sequence is circular
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86 -sformat1 string Input sequence format
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87 -iquery1 string Input query fields or ID list
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88 -ioffset1 integer Input start position offset
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89 -sdbname1 string Database name
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90 -sid1 string Entryname
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91 -ufo1 string UFO features
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92 -fformat1 string Features format
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93 -fopenfile1 string Features file name
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94
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95 "-graph" associated qualifiers
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96 -gprompt boolean Graph prompting
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97 -gdesc string Graph description
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98 -gtitle string Graph title
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99 -gsubtitle string Graph subtitle
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100 -gxtitle string Graph x axis title
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101 -gytitle string Graph y axis title
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102 -goutfile string Output file for non interactive displays
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103 -gdirectory string Output directory
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104
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105 "-outfile" associated qualifiers
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106 -odirectory string Output directory
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107
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108 General qualifiers:
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109 -auto boolean Turn off prompts
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110 -stdout boolean Write first file to standard output
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111 -filter boolean Read first file from standard input, write
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112 first file to standard output
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113 -options boolean Prompt for standard and additional values
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114 -debug boolean Write debug output to program.dbg
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115 -verbose boolean Report some/full command line options
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116 -help boolean Report command line options and exit. More
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117 information on associated and general
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118 qualifiers can be found with -help -verbose
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119 -warning boolean Report warnings
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120 -error boolean Report errors
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121 -fatal boolean Report fatal errors
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122 -die boolean Report dying program messages
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123 -version boolean Report version number and exit
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124
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125 Input file format
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126
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127 The database definitions for following commands are available at
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128 http://soap.g-language.org/kbws/embossrc
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129
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130 ggcskew reads one or more nucleotide sequences.
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131
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132 Output file format
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133
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134 The output from ggcskew is to a plain text file or the EMBOSS graphics
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135 device.
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136
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137 File: nc_000913.ggcskew
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138
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139 Sequence: NC_000913
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140 location,GC skew
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141 0,-0.035529
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142 10000,-0.039648
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143 20000,-0.049791
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144 30000,0.005072
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145 40000,-0.063483
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146 50000,-0.030256
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147 60000,0.011875
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148 70000,-0.029478
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149
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150 [Part of this file has been deleted for brevity]
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151
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152 4530000,-0.017164
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153 4540000,-0.036140
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154 4550000,-0.028166
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155 4560000,0.012166
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156 4570000,-0.040486
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157 4580000,-0.020692
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158 4590000,-0.043920
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159 4600000,-0.026363
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160 4610000,-0.022778
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161 4620000,-0.049396
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162
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163
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164 Data files
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165
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166 None.
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167
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168 Notes
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169
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170 None.
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171
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172 References
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173
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174 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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175 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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176 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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177
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178 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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179 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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180 31, 7.
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181
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182 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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183 Analysis Environment with REST and SOAP Web Service Interfaces,
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184 Nucleic Acids Res., 38, W700-W705.
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185
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186 Warnings
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187
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188 None.
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189
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190 Diagnostic Error Messages
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191
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192 None.
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193
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194 Exit status
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195
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196 It always exits with a status of 0.
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197
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198 Known bugs
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199
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200 None.
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201
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202 See also
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203
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204 ggcwin Calculates the GC content along the given genome
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205 ggeneskew Calculate the gene strand bias of the given genome
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206 ggenomicskew Calculates the GC skew in different regions of the given genom
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207
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208 Author(s)
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209
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210 Hidetoshi Itaya (celery@g-language.org)
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211 Institute for Advanced Biosciences, Keio University
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212 252-0882 Japan
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213
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214 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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215 Institute for Advanced Biosciences, Keio University
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216 252-0882 Japan
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217
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218 History
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219
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220 2012 - Written by Hidetoshi Itaya
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221 2013 - Fixed by Hidetoshi Itaya
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222
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223 Target users
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224
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225 This program is intended to be used by everyone and everything, from
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226 naive users to embedded scripts.
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227
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228 Comments
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229
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230 None.
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231
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