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1 gwvalue
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2 Function
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3
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4 Calculate the 'relative adaptiveness of each codon' (W)
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5
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6 Description
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7
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8 gwvalue calculates the 'relative adaptiveness of each codon' (W value)
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9 which is essential in CAI analysis. W value is calculated by setting the
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10 best codon to 1 and calculating the proportion of the other codons.
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11
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12 G-language SOAP service is provided by the
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13 Institute for Advanced Biosciences, Keio University.
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14 The original web service is located at the following URL:
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15
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16 http://www.g-language.org/wiki/soap
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17
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18 WSDL(RPC/Encoded) file is located at:
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19
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20 http://soap.g-language.org/g-language.wsdl
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21
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22 Documentation on G-language Genome Analysis Environment methods are
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23 provided at the Document Center
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24
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25 http://ws.g-language.org/gdoc/
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26
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27 Usage
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28
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29 Here is a sample session with gwvalue
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30
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31 % gwvalue refseqn:NC_000913
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32 Calculate the 'relative adaptiveness of each codon' (W)
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33 Codon usage output file [nc_000913.gwvalue]:
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34
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35 Go to the input files for this example
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36 Go to the output files for this example
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37
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38 Command line arguments
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39
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40 Standard (Mandatory) qualifiers:
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41 [-sequence] seqall Nucleotide sequence(s) filename and optional
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42 format, or reference (input USA)
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43 [-outfile] outfile [*.gwvalue] Codon usage output file
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44
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45 Additional (Optional) qualifiers: (none)
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46 Advanced (Unprompted) qualifiers:
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47 -include string [ribosomal.*protein] Regular expression to
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48 include genes in a reference set a reference
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49 set in several studies are in-built 1:
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50 Nakamura and Tabata, 2: Sharp and Li, 3:
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51 Sakai et al. (Any string)
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52 -exclude string [[Mm]itochondrial] Regular expression to
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53 exclude genes from a reference set (Any
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54 string)
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55 -[no]accid boolean [Y] Include to use sequence accession ID as
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56 query
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57
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58 Associated qualifiers:
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59
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60 "-sequence" associated qualifiers
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61 -sbegin1 integer Start of each sequence to be used
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62 -send1 integer End of each sequence to be used
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63 -sreverse1 boolean Reverse (if DNA)
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64 -sask1 boolean Ask for begin/end/reverse
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65 -snucleotide1 boolean Sequence is nucleotide
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66 -sprotein1 boolean Sequence is protein
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67 -slower1 boolean Make lower case
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68 -supper1 boolean Make upper case
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69 -scircular1 boolean Sequence is circular
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70 -sformat1 string Input sequence format
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71 -iquery1 string Input query fields or ID list
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72 -ioffset1 integer Input start position offset
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73 -sdbname1 string Database name
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74 -sid1 string Entryname
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75 -ufo1 string UFO features
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76 -fformat1 string Features format
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77 -fopenfile1 string Features file name
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78
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79 "-outfile" associated qualifiers
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80 -odirectory2 string Output directory
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81
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82 General qualifiers:
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83 -auto boolean Turn off prompts
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84 -stdout boolean Write first file to standard output
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85 -filter boolean Read first file from standard input, write
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86 first file to standard output
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87 -options boolean Prompt for standard and additional values
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88 -debug boolean Write debug output to program.dbg
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89 -verbose boolean Report some/full command line options
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90 -help boolean Report command line options and exit. More
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91 information on associated and general
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92 qualifiers can be found with -help -verbose
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93 -warning boolean Report warnings
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94 -error boolean Report errors
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95 -fatal boolean Report fatal errors
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96 -die boolean Report dying program messages
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97 -version boolean Report version number and exit
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98
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99 Input file format
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100
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101 The database definitions for following commands are available at
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102 http://soap.g-language.org/kbws/embossrc
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103
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104 gwvalue reads one or more nucleotide sequences.
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105
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106 Output file format
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107
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108 The output from gwvalue is to a plain text file.
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109
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110 File: nc_000913.gwvalue
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111
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112 Sequence: NC_000913
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113 Reference set of highly expressed genes
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114 product
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115 30S ribosomal subunit protein S20
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116 30S ribosomal subunit protein S2
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117 ribosomal protein S12 methylthiotransferase; radical SAM superfamily
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118 ribosomal protein S6 modification protein
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119 30S ribosomal subunit protein S1
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120 ribosomal-protein-S5-alanine N-acetyltransferase
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121 50S ribosomal subunit protein L32
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122
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123 [Part of this file has been deleted for brevity]
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124
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125 T,acc,1.0000
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126 T,acg,0.2234
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127 T,act,0.9734
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128 V,gta,0.4960
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129 V,gtc,0.2281
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130 V,gtg,0.3422
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131 V,gtt,1.0000
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132 W,tgg,1.0000
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133 Y,tac,1.0000
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134 Y,tat,0.5310
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135
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136
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137 Data files
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138
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139 None.
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140
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141 Notes
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142
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143 None.
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144
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145 References
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146
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147 Sharp PM et al. (2005) Variation in the strength of selected codon usage
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148 bias among bacteria, Nucleic Acids Res. 33(4):1141-1153
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149
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150 Sakai et al. (2001) Correlation between Shine--Dalgarno sequence
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151 conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170.
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152
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153 Nakamura and Tabata (1997) Codon-anticodon assignment and detection of
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154 codon usage trends in seven microbial genomes, Microb.Comp.Genomics
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155 2:299-312.
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156
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157 Sharp and Li (1987) The codon Adaptation Index--a measure of directional
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158 synonymous codon usage bias, and its potential applications, Nucleic
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159 Acids Res. 15:1281-1295.
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160
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161 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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162 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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163 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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164
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165 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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166 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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167 31, 7.
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168
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169 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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170 Analysis Environment with REST and SOAP Web Service Interfaces,
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171 Nucleic Acids Res., 38, W700-W705.
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172
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173 Warnings
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174
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175 None.
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176
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177 Diagnostic Error Messages
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178
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179 None.
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180
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181 Exit status
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182
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183 It always exits with a status of 0.
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184
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185 Known bugs
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186
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187 None.
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188
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189 See also
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190
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191 genc Calculate the effective number of codons (Nc)
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192 gew Calculate a measure of synonymous codon usage evenness (Ew)
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193 gfop Calculate the frequency of optimal codons (Fop)
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194 gscs Calculates the scaled chi-square
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195
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196 Author(s)
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197
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198 Hidetoshi Itaya (celery@g-language.org)
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199 Institute for Advanced Biosciences, Keio University
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200 252-0882 Japan
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201
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202 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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203 Institute for Advanced Biosciences, Keio University
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204 252-0882 Japan
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205
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206 History
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207
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208 2012 - Written by Hidetoshi Itaya
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209 2013 - Fixed by Hidetoshi Itaya
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210
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211 Target users
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212
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213 This program is intended to be used by everyone and everything, from
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214 naive users to embedded scripts.
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215
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216 Comments
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217
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218 None.
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219
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