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1 gsvalue
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2 Function
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3
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4 Calculate the strength of selected codon usage bias (S)
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5
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6 Description
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7
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8 gsvalue calculates the strength of selected codon usage bias (S), also
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9 known as Sharp's S index. Using four codon pairs that are recognized by the
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10 same tRNA anticodon, namely, Phe(UUC and UUU), Ile(AUC and AUU), Tyr(UAC and
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11 UAU), and Asn(AAC and AAU), since the former in each of the pairs has
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12 stronger Watson-Crick pairing, selection towards the former codon can be
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13 observed for highly expressed genes. S index is therefore the weighted
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14 average of such bias, giving an over-all value for a genome, indicating its
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15 strength of selected codon usage bias. See Sharp et al. (2005) for details.
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16 Sharp originally defined 40 genes as the highly expressed gene group, with
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17 tufA, tsf, fusA, rplA-rplF, rplI-rplT, rpsB-rpsT. Since the identificaiton
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18 of these genes is not convenient for computational automation, by default,
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19 this method uses ribosomal proteins as the highly expressed gene group,
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20 as used by Viera-silva and Rocha (2010).
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21 However, Sharp's gene group can be optionally used with -sharp option.
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22 With this option, all of the 40 genes must be named accordingly in the given
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23 genome file.
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24
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25 G-language SOAP service is provided by the
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26 Institute for Advanced Biosciences, Keio University.
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27 The original web service is located at the following URL:
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28
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29 http://www.g-language.org/wiki/soap
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30
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31 WSDL(RPC/Encoded) file is located at:
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32
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33 http://soap.g-language.org/g-language.wsdl
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34
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35 Documentation on G-language Genome Analysis Environment methods are
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36 provided at the Document Center
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37
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38 http://ws.g-language.org/gdoc/
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39
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40 Usage
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41
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42 Here is a sample session with gsvalue
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43
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44 % gsvalue refseqn:NC_000913
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45 Calculate the strength of selected codon usage bias (S)
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46 Codon usage output file [nc_000913.gsvalue]:
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47
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48 Go to the input files for this example
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49 Go to the output files for this example
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50
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51 Command line arguments
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52
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53 Standard (Mandatory) qualifiers:
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54 [-sequence] seqall Nucleotide sequence(s) filename and optional
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55 format, or reference (input USA)
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56 [-outfile] outfile [*.gsvalue] Codon usage output file
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57
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58 Additional (Optional) qualifiers: (none)
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59 Advanced (Unprompted) qualifiers:
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60 -sharp boolean [N] Include to use the 40 genes used by
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61 Sharp instead of ribosomal proteins
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62 -[no]accid boolean [Y] Include to use sequence accession ID as
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63 query
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64
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65 Associated qualifiers:
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66
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67 "-sequence" associated qualifiers
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68 -sbegin1 integer Start of each sequence to be used
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69 -send1 integer End of each sequence to be used
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70 -sreverse1 boolean Reverse (if DNA)
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71 -sask1 boolean Ask for begin/end/reverse
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72 -snucleotide1 boolean Sequence is nucleotide
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73 -sprotein1 boolean Sequence is protein
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74 -slower1 boolean Make lower case
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75 -supper1 boolean Make upper case
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76 -scircular1 boolean Sequence is circular
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77 -sformat1 string Input sequence format
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78 -iquery1 string Input query fields or ID list
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79 -ioffset1 integer Input start position offset
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80 -sdbname1 string Database name
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81 -sid1 string Entryname
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82 -ufo1 string UFO features
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83 -fformat1 string Features format
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84 -fopenfile1 string Features file name
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85
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86 "-outfile" associated qualifiers
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87 -odirectory2 string Output directory
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88
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89 General qualifiers:
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90 -auto boolean Turn off prompts
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91 -stdout boolean Write first file to standard output
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92 -filter boolean Read first file from standard input, write
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93 first file to standard output
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94 -options boolean Prompt for standard and additional values
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95 -debug boolean Write debug output to program.dbg
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96 -verbose boolean Report some/full command line options
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97 -help boolean Report command line options and exit. More
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98 information on associated and general
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99 qualifiers can be found with -help -verbose
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100 -warning boolean Report warnings
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101 -error boolean Report errors
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102 -fatal boolean Report fatal errors
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103 -die boolean Report dying program messages
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104 -version boolean Report version number and exit
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105
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106 Input file format
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107
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108 The database definitions for following commands are available at
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109 http://soap.g-language.org/kbws/embossrc
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110
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111 gsvalue reads one or more nucleotide sequences.
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112
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113 Output file format
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114
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115 The output from gsvalue is to a plain text file.
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116
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117 File: nc_000913.gsvalue
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118
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119 Sequence: NC_000913 S-value: 1.23467100598485
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120
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121
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122 Data files
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123
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124 None.
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125
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126 Notes
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127
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128 None.
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129
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130 References
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131
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132 Sharp PM et al. (2005) "Variation in the strength of selected codon usage
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133 bias among bacteria", Nucleic Acids Research, 33(4):1141-1153
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134
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135 Vieira-Silva S and Rocha EPC (2010) "The systemic imprint of growth and its
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136 uses in ecological (meta)genomics", PLoS Genetics, 6(1):e1000808
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137
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138 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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139 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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140 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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141
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142 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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143 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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144 31, 7.
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145
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146 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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147 Analysis Environment with REST and SOAP Web Service Interfaces,
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148 Nucleic Acids Res., 38, W700-W705.
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149
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150 Warnings
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151
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152 None.
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153
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154 Diagnostic Error Messages
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155
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156 None.
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157
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158 Exit status
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159
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160 It always exits with a status of 0.
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161
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162 Known bugs
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163
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164 None.
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165
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166 See also
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167
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168 gcbi Calculates the codon bias index (CBI)
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169 gdelta_enc Calculate the codon usage bias related to translation optimization (delta ENC)
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170 gicdi Calculates the intrinsic codon deviation index (ICDI)
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171
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172 Author(s)
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173
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174 Hidetoshi Itaya (celery@g-language.org)
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175 Institute for Advanced Biosciences, Keio University
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176 252-0882 Japan
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177
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178 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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179 Institute for Advanced Biosciences, Keio University
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180 252-0882 Japan
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181
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182 History
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183
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184 2012 - Written by Hidetoshi Itaya
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185 2013 - Fixed by Hidetoshi Itaya
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186
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187 Target users
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188
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189 This program is intended to be used by everyone and everything, from
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190 naive users to embedded scripts.
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191
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192 Comments
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193
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194 None.
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195
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