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1 gicdi
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2 Function
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3
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4 Calculates the intrinsic codon deviation index (ICDI)
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5
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6 Description
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7
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8 gicdi calculates the intrinsic codon deviation index (ICDI). ICDI is a
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9 measure to estimate codon bias of genes from species in which optimal
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10 codons are not known. It is known to show high correlation with other
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11 indices such as CBI and ENC. A gene using only one codon for each amino
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12 acid will have an ICDI of 1, and a gene using every codon equally for
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13 each amino acid will have an ICDI of 0.
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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 gicdi
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33
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34 % gicdi refseqn:NC_000913
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35 Calculates the intrinsic codon deviation index (ICDI)
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36 Codon usage output file [nc_000913.gicdi]:
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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 [*.gicdi] 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 -translate boolean [N] Include when translating using standard
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51 codon table
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52 -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
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53 expression to delete key (Any string)
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54 -[no]accid boolean [Y] Include to use sequence accession ID as
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55 query
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56
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57 Associated qualifiers:
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58
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59 "-sequence" associated qualifiers
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60 -sbegin1 integer Start of each sequence to be used
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61 -send1 integer End of each sequence to be used
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62 -sreverse1 boolean Reverse (if DNA)
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63 -sask1 boolean Ask for begin/end/reverse
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64 -snucleotide1 boolean Sequence is nucleotide
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65 -sprotein1 boolean Sequence is protein
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66 -slower1 boolean Make lower case
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67 -supper1 boolean Make upper case
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68 -scircular1 boolean Sequence is circular
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69 -sformat1 string Input sequence format
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70 -iquery1 string Input query fields or ID list
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71 -ioffset1 integer Input start position offset
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72 -sdbname1 string Database name
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73 -sid1 string Entryname
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74 -ufo1 string UFO features
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75 -fformat1 string Features format
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76 -fopenfile1 string Features file name
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77
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78 "-outfile" associated qualifiers
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79 -odirectory2 string Output directory
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80
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81 General qualifiers:
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82 -auto boolean Turn off prompts
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83 -stdout boolean Write first file to standard output
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84 -filter boolean Read first file from standard input, write
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85 first file to standard output
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86 -options boolean Prompt for standard and additional values
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87 -debug boolean Write debug output to program.dbg
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88 -verbose boolean Report some/full command line options
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89 -help boolean Report command line options and exit. More
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90 information on associated and general
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91 qualifiers can be found with -help -verbose
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92 -warning boolean Report warnings
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93 -error boolean Report errors
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94 -fatal boolean Report fatal errors
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95 -die boolean Report dying program messages
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96 -version boolean Report version number and exit
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97
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98 Input file format
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99
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100 The database definitions for following commands are available at
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101 http://soap.g-language.org/kbws/embossrc
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102
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103 gicdi reads one or more nucleotide sequences.
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104
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105 Output file format
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106
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107 The output from gicdi is to a plain text file.
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108
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109 File: nc_000913.gicdi
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110
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111 Sequence: NC_000913
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112 icdi,gene
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113 0.8192,thrL
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114 0.1258,thrA
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115 0.1127,thrB
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116 0.1689,thrC
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117 0.3099,yaaX
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118 0.2030,yaaA
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119 0.1600,yaaJ
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120 0.3533,talB
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121
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122 [Part of this file has been deleted for brevity]
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123
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124 0.2203,yjjX
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125 0.2719,ytjC
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126 0.1377,rob
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127 0.2647,creA
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128 0.1944,creB
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129 0.1733,creC
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130 0.1926,creD
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131 0.2728,arcA
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132 0.5171,yjjY
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133 0.2434,yjtD
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134
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135
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136 Data files
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137
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138 None.
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139
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140 Notes
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141
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142 None.
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143
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144 References
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145
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146 Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
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147 usage bias, J Mol Evol, 47(3):268-74.
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148
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149 Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in
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150 yeast cytochrome c-encoding genes, Gene, 139:43-49.
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151
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152 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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153 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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154 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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155
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156 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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157 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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158 31, 7.
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159
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160 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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161 Analysis Environment with REST and SOAP Web Service Interfaces,
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162 Nucleic Acids Res., 38, W700-W705.
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163
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164 Warnings
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165
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166 None.
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167
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168 Diagnostic Error Messages
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169
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170 None.
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171
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172 Exit status
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173
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174 It always exits with a status of 0.
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175
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176 Known bugs
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177
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178 None.
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179
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180 See also
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181
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182 gcbi Calculates the codon bias index (CBI)
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183 gdeltaenc Calculate the codon usage bias related to translation optimization
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184 (delta ENC)
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185 gsvalue Calculate the strength of selected codon usage bias (S)
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186
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187 Author(s)
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188
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189 Hidetoshi Itaya (celery@g-language.org)
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190 Institute for Advanced Biosciences, Keio University
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191 252-0882 Japan
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192
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193 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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194 Institute for Advanced Biosciences, Keio University
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195 252-0882 Japan
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196
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197 History
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198
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199 2012 - Written by Hidetoshi Itaya
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200 2013 - Fixed by Hidetoshi Itaya
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201
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202 Target users
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203
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204 This program is intended to be used by everyone and everything, from
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205 naive users to embedded scripts.
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206
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207 Comments
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208
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209 None.
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210
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