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1 gdeltagcskew
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2 Function
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3
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4 Calculate strand bias of bacterial genome using delta GC skew index
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5
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6 Description
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7
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8 gdeltagcskew calculates strand bias of bacterial genome using delta GC skew
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9 index, first proposed by Rocha et al. (2001), and further extended in 2006.
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10 Basic idea of delta GC skew index is to calculate the difference of GC skew
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11 in coding regions residing in leading and lagging strands. Rocha et al.
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12 (2001) calculates delta GC skew index using the third codon position of
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13 genes, and Rocha et al. (2006) modified to only use >fourfold degenerate
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14 codons.
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15
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16 G-language SOAP service is provided by the
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17 Institute for Advanced Biosciences, Keio University.
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18 The original web service is located at the following URL:
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19
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20 http://www.g-language.org/wiki/soap
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21
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22 WSDL(RPC/Encoded) file is located at:
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23
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24 http://soap.g-language.org/g-language.wsdl
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25
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26 Documentation on G-language Genome Analysis Environment methods are
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27 provided at the Document Center
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28
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29 http://ws.g-language.org/gdoc/
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30
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31 Usage
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32
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33 Here is a sample session with gdeltagcskew
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34
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35 % gdeltagcskew refseqn:NC_000913
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36 Calculate strand bias of bacterial genome using delta GC skew index
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37 Program compseq output file [nc_000913.gdeltagcskew]:
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38
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39 Go to the input files for this example
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40 Go to the output files for this example
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41
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42 Command line arguments
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43
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44 Standard (Mandatory) qualifiers:
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45 [-sequence] seqall Nucleotide sequence(s) filename and optional
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46 format, or reference (input USA)
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47 [-outfile] outfile [*.gdeltagcskew] Program compseq output file
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48
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49 Additional (Optional) qualifiers: (none)
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50 Advanced (Unprompted) qualifiers:
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51 -at boolean [N] Include when observing AT skew instead
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52 of GC skew
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53 -purine boolean [N] Include when observing purine (AG/TC)
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54 skew
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55 -keto boolean [N] Include when observing keto (TG/AC) skew
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56 -method selection [degenerate] Choose the nucleotides to use
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57 'degenerate', 'gc3', or 'all'
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58 -[no]accid boolean [Y] Include to use sequence accession ID as
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59 query
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60
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61 Associated qualifiers:
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62
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63 "-sequence" associated qualifiers
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64 -sbegin1 integer Start of each sequence to be used
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65 -send1 integer End of each sequence to be used
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66 -sreverse1 boolean Reverse (if DNA)
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67 -sask1 boolean Ask for begin/end/reverse
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68 -snucleotide1 boolean Sequence is nucleotide
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69 -sprotein1 boolean Sequence is protein
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70 -slower1 boolean Make lower case
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71 -supper1 boolean Make upper case
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72 -scircular1 boolean Sequence is circular
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73 -sformat1 string Input sequence format
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74 -iquery1 string Input query fields or ID list
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75 -ioffset1 integer Input start position offset
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76 -sdbname1 string Database name
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77 -sid1 string Entryname
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78 -ufo1 string UFO features
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79 -fformat1 string Features format
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80 -fopenfile1 string Features file name
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81
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82 "-outfile" associated qualifiers
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83 -odirectory2 string Output directory
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84
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85 General qualifiers:
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86 -auto boolean Turn off prompts
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87 -stdout boolean Write first file to standard output
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88 -filter boolean Read first file from standard input, write
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89 first file to standard output
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90 -options boolean Prompt for standard and additional values
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91 -debug boolean Write debug output to program.dbg
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92 -verbose boolean Report some/full command line options
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93 -help boolean Report command line options and exit. More
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94 information on associated and general
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95 qualifiers can be found with -help -verbose
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96 -warning boolean Report warnings
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97 -error boolean Report errors
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98 -fatal boolean Report fatal errors
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99 -die boolean Report dying program messages
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100 -version boolean Report version number and exit
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101
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102 Input file format
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103
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104 The database definitions for following commands are available at
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105 http://soap.g-language.org/kbws/embossrc
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106
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107 gdeltagcskew reads one or more nucleotide sequences.
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108
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109 Output file format
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110
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111 The output from gdeltagcskew is to a plain text file.
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112
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113 File: nc_000913.gdeltagcskew
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114
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115 Sequence: NC_000913 DELTA-GCskew -0.108937
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116
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117
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118 Data files
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119
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120 None.
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121
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122 Notes
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123
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124 None.
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125
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126 References
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127
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128 Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial
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129 Genomes, Molecular Biology and Evolution, 18(9):1789-1799
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130
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131 Rocha EPC et al. (2006) Similar compositional biases are caused by very
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132 different mutational effects, Genome Research, 16:1537-1547
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133
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134 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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135 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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136 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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137
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138 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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139 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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140 31, 7.
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141
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142 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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143 Analysis Environment with REST and SOAP Web Service Interfaces,
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144 Nucleic Acids Res., 38, W700-W705.
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145
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146 Warnings
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147
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148 None.
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149
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150 Diagnostic Error Messages
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151
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152 None.
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153
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154 Exit status
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155
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156 It always exits with a status of 0.
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157
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158 Known bugs
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159
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160 None.
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161
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162 See also
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163
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164 gb1 Calculate strand bias of bacterial genome using B1 index
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165 gb2 Calculate strand bias of bacterial genome using B2 index
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166 ggcsi GC Skew Index: an index for strand-specefic mutational bias
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167 gldabias Calculate strand bias of bacterial genome using linear
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168 discriminant analysis (LDA)
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169
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170 Author(s)
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171
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172 Hidetoshi Itaya (celery@g-language.org)
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173 Institute for Advanced Biosciences, Keio University
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174 252-0882 Japan
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175
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176 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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177 Institute for Advanced Biosciences, Keio University
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178 252-0882 Japan
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179
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180 History
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181
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182 2012 - Written by Hidetoshi Itaya
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183 2013 - Fixed by Hidetoshi Itaya
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184
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185 Target users
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186
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187 This program is intended to be used by everyone and everything, from
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188 naive users to embedded scripts.
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189
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190 Comments
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191
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192 None.
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193
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