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1 ggenomicskew
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2 Function
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3
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4 Calculates the GC skew in different regions of the given genome
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5
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6 Description
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7
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8 ggenomicskew calculates and plots the GC skew for the whole genome, coding
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9 regions, intergenic regions, and the third codon. This program is useful in
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10 visualizing various base composition bias within the genome. AT skew can be
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11 calculated instead of GC skew by toggling the -at qualifier.
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12
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13 G-language SOAP service is provided by the
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14 Institute for Advanced Biosciences, Keio University.
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15 The original web service is located at the following URL:
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16
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17 http://www.g-language.org/wiki/soap
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18
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19 WSDL(RPC/Encoded) file is located at:
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20
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21 http://soap.g-language.org/g-language.wsdl
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22
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23 Documentation on G-language Genome Analysis Environment methods are
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24 provided at the Document Center
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25
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26 http://ws.g-language.org/gdoc/
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27
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28 Usage
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29
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30 Here is a sample session with ggenomicskew
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31
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32 % ggenomicskew refseqn:NC_000913
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33 Calculates the GC skew in different regions of the given genome
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34 Program compseq output file (optional) [nc_000913.ggenomicskew]:
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35
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36 Go to the input files for this example
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37 Go to the output files for this example
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38
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39 Example 2
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40
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41 % ggenomicskew refseqn:NC_000913 -plot -graph png
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42 Calculates the GC skew in different regions of the given genome
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43 Created ggenomicskew.1.png
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44
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45 Go to the input files for this example
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46 Go to the output files for this example
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47
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48 Command line arguments
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49
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50 Standard (Mandatory) qualifiers (* if not always prompted):
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51 [-sequence] seqall Nucleotide sequence(s) filename and optional
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52 format, or reference (input USA)
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53 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
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54 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
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55 tek, tekt, none, data, xterm, png, gif, svg)
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56 * -outfile outfile [*.ggenomicskew] Program compseq output file
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57 (optional)
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58
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59 Additional (Optional) qualifiers: (none)
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60 Advanced (Unprompted) qualifiers:
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61 -divide integer [250] Window to divide into (Any integer
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62 value)
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63 -at boolean [N] Input 1 when observing AT skew instead
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64 of GC skew
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65 -[no]accid boolean [Y] Include to use sequence accession ID as
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66 query
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67 -plot toggle [N] Include to plot result
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68
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69 Associated qualifiers:
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70
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71 "-sequence" associated qualifiers
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72 -sbegin1 integer Start of each sequence to be used
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73 -send1 integer End of each sequence to be used
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74 -sreverse1 boolean Reverse (if DNA)
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75 -sask1 boolean Ask for begin/end/reverse
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76 -snucleotide1 boolean Sequence is nucleotide
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77 -sprotein1 boolean Sequence is protein
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78 -slower1 boolean Make lower case
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79 -supper1 boolean Make upper case
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80 -scircular1 boolean Sequence is circular
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81 -sformat1 string Input sequence format
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82 -iquery1 string Input query fields or ID list
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83 -ioffset1 integer Input start position offset
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84 -sdbname1 string Database name
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85 -sid1 string Entryname
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86 -ufo1 string UFO features
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87 -fformat1 string Features format
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88 -fopenfile1 string Features file name
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89
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90 "-graph" associated qualifiers
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91 -gprompt boolean Graph prompting
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92 -gdesc string Graph description
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93 -gtitle string Graph title
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94 -gsubtitle string Graph subtitle
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95 -gxtitle string Graph x axis title
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96 -gytitle string Graph y axis title
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97 -goutfile string Output file for non interactive displays
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98 -gdirectory string Output directory
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99
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100 "-outfile" associated qualifiers
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101 -odirectory string Output directory
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102
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103 General qualifiers:
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104 -auto boolean Turn off prompts
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105 -stdout boolean Write first file to standard output
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106 -filter boolean Read first file from standard input, write
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107 first file to standard output
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108 -options boolean Prompt for standard and additional values
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109 -debug boolean Write debug output to program.dbg
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110 -verbose boolean Report some/full command line options
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111 -help boolean Report command line options and exit. More
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112 information on associated and general
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113 qualifiers can be found with -help -verbose
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114 -warning boolean Report warnings
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115 -error boolean Report errors
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116 -fatal boolean Report fatal errors
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117 -die boolean Report dying program messages
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118 -version boolean Report version number and exit
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119
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120 Input file format
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121
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122 The database definitions for following commands are available at
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123 http://soap.g-language.org/kbws/embossrc
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124
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125 ggenomicskew reads one or more nucleotide sequences.
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126
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127 Output file format
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128
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129 The output from ggenomicskew is to a plain text file or the EMBOSS graphics device.
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130
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131 File: nc_000913.ggenomicskew
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132
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133 Sequence: NC_000913
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134 location,GC skew,coding,intergenic,third codon
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135 0,-0.036259,-0.040085,-0.034707,-0.141888,
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136 1,-0.031167,-0.035657,0.047953,-0.175758,
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137 2,-0.028670,-0.031139,-0.049143,-0.018466,
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138 3,-0.016647,-0.004656,-0.102616,0.086181,
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139 4,-0.041985,-0.029846,-0.088670,0.015291,
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140 5,-0.097093,-0.103813,-0.067275,-0.247401,
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141 6,-0.028028,-0.016363,-0.048806,-0.047332,
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142 7,-0.055805,-0.059329,-0.020071,-0.123271,
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143
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144 [Part of this file has been deleted for brevity]
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145
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146 241,0.000772,-0.012151,-0.063786,0.069585,
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147 242,-0.025787,-0.000384,-0.049143,0.029431,
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148 243,0.010516,0.008217,-0.030600,0.128657,
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149 244,-0.037115,-0.015134,0.017500,0.035398,
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150 245,-0.000317,0.006021,-0.047170,0.091549,
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151 246,-0.025417,-0.015190,-0.116608,0.044619,
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152 247,-0.038404,-0.035676,-0.135714,0.015375,
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153 248,-0.026246,-0.024240,-0.037190,-0.130118,
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154 249,-0.053371,-0.057225,-0.022472,-0.082167,
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155 250,-0.026316,0.166667,-0.151515,0.000000,
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156
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157
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158 Data files
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159
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160 None.
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161
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162 Notes
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163
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164 None.
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165
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166 References
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167
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168 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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169 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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170 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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171
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172 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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173 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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174 31, 7.
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175
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176 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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177 Analysis Environment with REST and SOAP Web Service Interfaces,
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178 Nucleic Acids Res., 38, W700-W705.
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179
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180 Warnings
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181
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182 None.
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183
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184 Diagnostic Error Messages
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185
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186 None.
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187
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188 Exit status
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189
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190 It always exits with a status of 0.
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191
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192 Known bugs
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193
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194 None.
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195
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196 See also
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197
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198 ggcskew Calculates the GC skew of the input sequence
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199 ggcwin Calculates the GC content along the given genome
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200 ggeneskew Calculate the gene strand bias of the given genome
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201
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202 Author(s)
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203
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204 Hidetoshi Itaya (celery@g-language.org)
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205 Institute for Advanced Biosciences, Keio University
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206 252-0882 Japan
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207
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208 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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209 Institute for Advanced Biosciences, Keio University
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210 252-0882 Japan
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211
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212 History
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213
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214 2012 - Written by Hidetoshi Itaya
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215 2013 - Fixed by Hidetoshi Itaya
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216
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217 Target users
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218
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219 This program is intended to be used by everyone and everything, from
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220 naive users to embedded scripts.
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221
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222 Comments
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223
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224 None.
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225
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