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1 ggeneskew
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2 Function
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3
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4 Calculate the gene strand bias 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 ggeneskew calculates and plots the strand bias of genes (or the GC skew
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9 within them). By default, this program visualizes the gene strand preference
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10 (1 for direct, -1 for complement strand), but by specifying -base option
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11 option, GC/AT/Purine/Keto skews of the coding regions or more specifically
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12 in the GC3 (third codon position) with -gctri option can be calculated.
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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 ggeneskew
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32
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33 % ggeneskew refseqn:NC_000913
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34 Calculate the gene strand bias of the given genome
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35 Program compseq output file (optional) [nc_000913.ggeneskew]:
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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 % ggeneskew refseqn:NC_000913 -plot -graph png
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43 Calculate the gene strand bias of the given genome
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44 Created ggeneskew.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 [*.ggeneskew] 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] Input 1 to calculate cumulative skew
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67 -base selection [none] Input 'gc', 'at', 'purine', or 'keto'
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68 for observing GC/AT/Purine/Keto skews
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69 -gctri boolean [N] Include to use only the third codon
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70 positions
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71 -[no]accid boolean [Y] Include to use sequence accession ID as
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72 query
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73 -plot toggle [N] Include to plot result
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74
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75 Associated qualifiers:
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76
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77 "-sequence" associated qualifiers
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78 -sbegin1 integer Start of each sequence to be used
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79 -send1 integer End of each sequence to be used
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80 -sreverse1 boolean Reverse (if DNA)
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81 -sask1 boolean Ask for begin/end/reverse
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82 -snucleotide1 boolean Sequence is nucleotide
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83 -sprotein1 boolean Sequence is protein
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84 -slower1 boolean Make lower case
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85 -supper1 boolean Make upper case
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86 -scircular1 boolean Sequence is circular
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87 -sformat1 string Input sequence format
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88 -iquery1 string Input query fields or ID list
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89 -ioffset1 integer Input start position offset
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90 -sdbname1 string Database name
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91 -sid1 string Entryname
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92 -ufo1 string UFO features
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93 -fformat1 string Features format
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94 -fopenfile1 string Features file name
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95
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96 "-graph" associated qualifiers
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97 -gprompt boolean Graph prompting
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98 -gdesc string Graph description
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99 -gtitle string Graph title
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100 -gsubtitle string Graph subtitle
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101 -gxtitle string Graph x axis title
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102 -gytitle string Graph y axis title
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103 -goutfile string Output file for non interactive displays
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104 -gdirectory string Output directory
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105
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106 "-outfile" associated qualifiers
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107 -odirectory string Output directory
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108
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109 General qualifiers:
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110 -auto boolean Turn off prompts
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111 -stdout boolean Write first file to standard output
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112 -filter boolean Read first file from standard input, write
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113 first file to standard output
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114 -options boolean Prompt for standard and additional values
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115 -debug boolean Write debug output to program.dbg
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116 -verbose boolean Report some/full command line options
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117 -help boolean Report command line options and exit. More
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118 information on associated and general
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119 qualifiers can be found with -help -verbose
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120 -warning boolean Report warnings
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121 -error boolean Report errors
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122 -fatal boolean Report fatal errors
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123 -die boolean Report dying program messages
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124 -version boolean Report version number and exit
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125
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126 Input file format
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127
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128 The database definitions for following commands are available at
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129 http://soap.g-language.org/kbws/embossrc
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130
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131 ggeneskew reads one or more nucleotide sequences.
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132
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133 Output file format
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134
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135 The output from ggeneskew is to a plain text file or the EMBOSS graphics
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136 device.
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137
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138 File: nc_000913.ggeneskew
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139
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140 Sequence: NC_000913
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141 location,gene None skew
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142 190,0.294118
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143 337,-0.058914
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144 2801,-0.120000
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145 3734,-0.070588
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146 5234,0.037500
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147 5683,0.020725
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148 6529,0.032765
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149 8238,-0.028226
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150
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151 [Part of this file has been deleted for brevity]
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152
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153 4631820,-0.093407
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154 4632464,-0.006479
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155 4633544,-0.120690
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156 4634030,-0.060367
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157 4634719,-0.104167
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158 4636201,-0.144560
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159 4637613,0.010929
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160 4638425,0.200000
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161 4638965,-0.081871
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162 ,
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163
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164
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165 Data files
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166
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167 None.
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168
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169 Notes
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170
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171 None.
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172
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173 References
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174
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175 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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176 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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177 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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178
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179 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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180 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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181 31, 7.
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182
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183 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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184 Analysis Environment with REST and SOAP Web Service Interfaces,
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185 Nucleic Acids Res., 38, W700-W705.
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186
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187 Warnings
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188
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189 None.
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190
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191 Diagnostic Error Messages
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192
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193 None.
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194
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195 Exit status
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196
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197 It always exits with a status of 0.
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198
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199 Known bugs
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200
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201 None.
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202
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203 See also
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204
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205 ggcskew Calculates the GC skew of the input sequence
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206 ggcwin Calculates the GC content along the given genome
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207 ggenomicskew Calculates the GC skew in different regions of the given genom
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208
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209 Author(s)
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210
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211 Hidetoshi Itaya (celery@g-language.org)
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212 Institute for Advanced Biosciences, Keio University
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213 252-0882 Japan
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214
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215 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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216 Institute for Advanced Biosciences, Keio University
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217 252-0882 Japan
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218
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219 History
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220
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221 2012 - Written by Hidetoshi Itaya
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222 2013 - Fixed by Hidetoshi Itaya
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223
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224 Target users
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225
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226 This program is intended to be used by everyone and everything, from
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227 naive users to embedded scripts.
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228
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229 Comments
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230
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231 None.
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232
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