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1 gp2
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2 Function
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3
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4 Calculate the P2 index of each gene
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5
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6 Description
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7
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8 gp2 calculates the P2 index for each gene. This index describes
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9 the proportion of codons conforming to the intermediate strength of
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10 codon-anticodon interaction energy rule of Grosjean and Fiers:
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11 P2 = (WWC+SSU)/(WWY+SSY) where W = A or U, S = C or G, and Y = C or U.
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12 It indicates the efficiency of the codon-anticodon interaction, and has
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13 been used as an indicator of the presence of translational selection.
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14
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15 G-language SOAP service is provided by the
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16 Institute for Advanced Biosciences, Keio University.
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17 The original web service is located at the following URL:
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18
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19 http://www.g-language.org/wiki/soap
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20
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21 WSDL(RPC/Encoded) file is located at:
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22
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23 http://soap.g-language.org/g-language.wsdl
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24
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25 Documentation on G-language Genome Analysis Environment methods are
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26 provided at the Document Center
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27
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28 http://ws.g-language.org/gdoc/
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29
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30 Usage
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31
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32 Here is a sample session with gp2
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33
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34 % gp2 refseqn:NC_000913
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35 Calculate the P2 index of each gene
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36 Codon usage output file [nc_000913.gp2]:
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37
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38 Go to the input files for this example
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39 Go to the output files for this example
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40
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41 Command line arguments
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42
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43 Standard (Mandatory) qualifiers:
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44 [-sequence] seqall Nucleotide sequence(s) filename and optional
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45 format, or reference (input USA)
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46 [-outfile] outfile [*.gp2] Codon usage output file
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47
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48 Additional (Optional) qualifiers: (none)
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49 Advanced (Unprompted) qualifiers:
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50 -[no]accid boolean [Y] Include to use sequence accession ID as
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51 query
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52
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53 Associated qualifiers:
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54
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55 "-sequence" associated qualifiers
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56 -sbegin1 integer Start of each sequence to be used
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57 -send1 integer End of each sequence to be used
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58 -sreverse1 boolean Reverse (if DNA)
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59 -sask1 boolean Ask for begin/end/reverse
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60 -snucleotide1 boolean Sequence is nucleotide
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61 -sprotein1 boolean Sequence is protein
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62 -slower1 boolean Make lower case
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63 -supper1 boolean Make upper case
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64 -scircular1 boolean Sequence is circular
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65 -sformat1 string Input sequence format
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66 -iquery1 string Input query fields or ID list
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67 -ioffset1 integer Input start position offset
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68 -sdbname1 string Database name
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69 -sid1 string Entryname
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70 -ufo1 string UFO features
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71 -fformat1 string Features format
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72 -fopenfile1 string Features file name
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73
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74 "-outfile" associated qualifiers
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75 -odirectory2 string Output directory
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76
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77 General qualifiers:
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78 -auto boolean Turn off prompts
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79 -stdout boolean Write first file to standard output
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80 -filter boolean Read first file from standard input, write
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81 first file to standard output
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82 -options boolean Prompt for standard and additional values
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83 -debug boolean Write debug output to program.dbg
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84 -verbose boolean Report some/full command line options
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85 -help boolean Report command line options and exit. More
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86 information on associated and general
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87 qualifiers can be found with -help -verbose
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88 -warning boolean Report warnings
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89 -error boolean Report errors
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90 -fatal boolean Report fatal errors
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91 -die boolean Report dying program messages
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92 -version boolean Report version number and exit
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93
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94 Input file format
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95
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96 The database definitions for following commands are available at
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97 http://soap.g-language.org/kbws/embossrc
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98
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99 gp2 reads one or more nucleotide sequences.
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100
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101 Output file format
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102
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103 The output from gp2 is to a plain text file.
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104
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105 File: nc_000913.gp2
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106
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107 Sequence: NC_000913
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108 P2,gene
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109 0.4444,thrL
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110 0.4234,thrA
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111 0.4565,thrB
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112 0.5156,thrC
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113 0.4074,yaaX
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114 0.4494,yaaA
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115 0.3621,yaaJ
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116 0.6832,talB
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117
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118 [Part of this file has been deleted for brevity]
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119
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120 0.3692,yjjX
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121 0.4912,ytjC
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122 0.4271,rob
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123 0.4318,creA
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124 0.3065,creB
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125 0.3851,creC
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126 0.4320,creD
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127 0.6395,arcA
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128 0.7857,yjjY
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129 0.3333,yjtD
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130
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131
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132 Data files
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133
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134 None.
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135
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136 Notes
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137
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138 None.
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139
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140 References
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141
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142 Gouy M, Gautier C. (1982) Codon usage in bacteria: correlation with gene
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143 expressivity, Nucleic Acids Res, 10(22):7055-74.
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144
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145 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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146 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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147 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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148
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149 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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150 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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151 31, 7.
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152
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153 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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154 Analysis Environment with REST and SOAP Web Service Interfaces,
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155 Nucleic Acids Res., 38, W700-W705.
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156
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157 Warnings
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158
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159 None.
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160
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161 Diagnostic Error Messages
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162
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163 None.
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164
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165 Exit status
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166
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167 It always exits with a status of 0.
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168
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169 Known bugs
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170
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171 None.
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172
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173 See also
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174
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175 gcai Calculate codon adaptation index for each gene
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176 gphx Identify predicted highly expressed gene
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177
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178 Author(s)
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179
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180 Hidetoshi Itaya (celery@g-language.org)
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181 Institute for Advanced Biosciences, Keio University
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182 252-0882 Japan
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183
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184 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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185 Institute for Advanced Biosciences, Keio University
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186 252-0882 Japan
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187
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188 History
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189
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190 2012 - Written by Hidetoshi Itaya
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191 2013 - Fixed by Hidetoshi Itaya
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192
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193 Target users
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194
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195 This program is intended to be used by everyone and everything, from
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196 naive users to embedded scripts.
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197
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198 Comments
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199
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200 None.
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201
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