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1 ggcsi
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2 Function
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3
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4 GC Skew Index: an index for strand-specific mutational bias
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5
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6 Description
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7
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8 ggcsi calculates the GC Skew Index (GCSI) of the given circular bacterial
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9 genome. GCSI quantifies the degree of GC Skew. In other words, this index
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10 represents the degree of strand-specific mutational bias in bacterial
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11 genomes, caused by replicational selection.
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12 GCSI is calculated by the following formula:
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13
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14 GCSI = sqrt((SA/6000) * (dist/600))
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15
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16 where SA is the spectral amplitude of Fourier power spectrum at 1Hz,
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17 and dist is the normalized Euclidean distance between the vertices of
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18 cumulative GC skew.
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19
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20 GCSI ranges from 0 (no observable skew) to 1 (strong skew), and Archaeal
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21 genomes that have multiple replication origins and therefore have no
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22 observable skew mostly have GCSI below 0.05. Escherichia coli genome has
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23 values around 0.10.
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24
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25 Version 1 of GCSI required fixed number of windows (4096), but the new GCSI
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26 version 2 (also known as generalized GCSI: gGCSI) is invariant of the number
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27 of windows. GCSI version 1 is calculated as an arithmetic mean (as opposed
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28 to the geometric mean of gGCSI) of SR (spectral ratio, the signal-to-noise
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29 ratio of 1Hz power spectrum) and dist.
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30
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31 G-language SOAP service is provided by the
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32 Institute for Advanced Biosciences, Keio University.
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33 The original web service is located at the following URL:
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34
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35 http://www.g-language.org/wiki/soap
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36
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37 WSDL(RPC/Encoded) file is located at:
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38
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39 http://soap.g-language.org/g-language.wsdl
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40
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41 Documentation on G-language Genome Analysis Environment methods are
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42 provided at the Document Center
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43
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44 http://ws.g-language.org/gdoc/
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45
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46 Usage
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47
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48 Here is a sample session with ggcsi
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49
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50 % ggcsi refseqn:NC_000913
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51 GC Skew Index: an index for strand-specific mutational bias
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52 Program compseq output file [nc_000913.ggcsi]:
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53
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54 Go to the input files for this example
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55 Go to the output files for this example
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56
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57 Command line arguments
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58
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59 Standard (Mandatory) qualifiers:
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60 [-sequence] seqall Nucleotide sequence(s) filename and optional
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61 format, or reference (input USA)
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62 [-outfile] outfile [*.ggcsi] Program compseq output file
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63
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64 Additional (Optional) qualifiers: (none)
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65 Advanced (Unprompted) qualifiers:
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66 -gcsi selection [2] GCSI version to use
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67 -window integer [4096] Number of windows. Must be a power of
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68 2 (Any integer value)
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69 -purine boolean [N] Use purine skew for calculation
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70 -keto boolean [N] Use keto skew for calculation
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71 -at boolean [N] Use AT skew for calculation
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72 -pval boolean [N] Calculate p-value when GCSI version 2 is
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73 selected
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74 -[no]accid boolean [Y] Include to use sequence accession ID as
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75 query
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76
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77 Associated qualifiers:
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78
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79 "-sequence" associated qualifiers
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80 -sbegin1 integer Start of each sequence to be used
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81 -send1 integer End of each sequence to be used
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82 -sreverse1 boolean Reverse (if DNA)
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83 -sask1 boolean Ask for begin/end/reverse
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84 -snucleotide1 boolean Sequence is nucleotide
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85 -sprotein1 boolean Sequence is protein
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86 -slower1 boolean Make lower case
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87 -supper1 boolean Make upper case
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88 -scircular1 boolean Sequence is circular
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89 -sformat1 string Input sequence format
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90 -iquery1 string Input query fields or ID list
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91 -ioffset1 integer Input start position offset
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92 -sdbname1 string Database name
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93 -sid1 string Entryname
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94 -ufo1 string UFO features
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95 -fformat1 string Features format
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96 -fopenfile1 string Features file name
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97
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98 "-outfile" associated qualifiers
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99 -odirectory2 string Output directory
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100
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101 General qualifiers:
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102 -auto boolean Turn off prompts
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103 -stdout boolean Write first file to standard output
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104 -filter boolean Read first file from standard input, write
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105 first file to standard output
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106 -options boolean Prompt for standard and additional values
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107 -debug boolean Write debug output to program.dbg
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108 -verbose boolean Report some/full command line options
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109 -help boolean Report command line options and exit. More
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110 information on associated and general
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111 qualifiers can be found with -help -verbose
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112 -warning boolean Report warnings
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113 -error boolean Report errors
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114 -fatal boolean Report fatal errors
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115 -die boolean Report dying program messages
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116 -version boolean Report version number and exit
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117
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118 Input file format
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119
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120 The database definitions for following commands are available at
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121 http://soap.g-language.org/kbws/embossrc
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122
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123 ggcsi reads one or more nucleotide sequences.
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124
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125 Output file format
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126
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127 The output from ggcsi is to a plain text file.
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128
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129 File: nc_000913.ggcsi
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130
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131 Sequence: NC_000913 GCSI: 0.0966615833014818 SA: 487.218569030757 DIST: 69.037726
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132
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133
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134 Data files
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135
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136 None.
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137
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138 Notes
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139
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140 None.
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141
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142 References
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143
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144 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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145 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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146 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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147
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148 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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149 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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150 31, 7.
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151
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152 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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153 Analysis Environment with REST and SOAP Web Service Interfaces,
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154 Nucleic Acids Res., 38, W700-W705.
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155
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156 Warnings
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157
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158 None.
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159
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160 Diagnostic Error Messages
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161
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162 None.
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163
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164 Exit status
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165
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166 It always exits with a status of 0.
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167
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168 Known bugs
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169
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170 None.
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171
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172 See also
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173
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174 gb1 Calculate strand bias of bacterial genome using B1 index
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175 gb2 Calculate strand bias of bacterial genome using B2 index
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176 gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
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177 index
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178 gldabias Calculate strand bias of bacterial genome using linear
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179 discriminant analysis (LDA)
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180
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181 Author(s)
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182
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183 Hidetoshi Itaya (celery@g-language.org)
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184 Institute for Advanced Biosciences, Keio University
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185 252-0882 Japan
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186
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187 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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188 Institute for Advanced Biosciences, Keio University
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189 252-0882 Japan
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190
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191 History
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192
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193 2012 - Written by Hidetoshi Itaya
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194 2013 - Fixed by Hidetoshi Itaya
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195
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196 Target users
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197
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198 This program is intended to be used by everyone and everything, from
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199 naive users to embedded scripts.
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200
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201 Comments
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202
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203 None.
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204
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