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0
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1 genc
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2 Function
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3
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4 Calculate the effective number of codons (Nc)
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5
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6 Description
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7
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8 genc calculates the effective number of codons (ENC|Nc). ENC is a measure
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9 for species-independent codon usage bias. Some measures including CAI are
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10 species-dependent as optimal codons differ. ENC assigns a gene a number
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11 between 20 to 61 where 20 indicates that one codon is used for each amino
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12 acid and 61 indicates that each codon is used equally throughout the
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13 protein sequence.
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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 genc
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33
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34 % genc refseqn:NC_000913
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35 Calculate the effective number of codons (Nc)
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36 Codon usage output file [nc_000913.genc]:
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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 [*.genc] 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 translates 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 (i.e. amino acids
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54 and nucleotides) (Any 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 genc 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 genc is to a plain text file.
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109
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110 File: nc_000913.genc
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111
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112 Sequence: NC_000913
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113 enc,gene
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114 ,thrL
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115 48.41,thrA
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116 54.13,thrB
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117 46.18,thrC
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118 51.65,yaaX
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119 45.71,yaaA
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120 48.54,yaaJ
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121 36.83,talB
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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 51.43,yjjX
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126 46.61,ytjC
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127 49.83,rob
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128 47.74,creA
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129 50.63,creB
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130 51.39,creC
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131 48.42,creD
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132 41.53,arcA
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133 61,yjjY
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134 53.63,yjtD
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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 Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
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148 usage bias, J Mol Evol, 47(3):268-74.
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149
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150 Wright F. (1990) The 'effective number of codons' used in a gene, Gene,
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151 87:23-29.
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152
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153 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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154 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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155 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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156
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157 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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158 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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159 31, 7.
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160
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161 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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162 Analysis Environment with REST and SOAP Web Service Interfaces,
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163 Nucleic Acids Res., 38, W700-W705.
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164
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165 Warnings
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166
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167 None.
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168
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169 Diagnostic Error Messages
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170
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171 None.
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172
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173 Exit status
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174
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175 It always exits with a status of 0.
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176
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177 Known bugs
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178
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179 None.
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180
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181 See also
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182
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183 gew Calculate a measure of synonymous codon usage evenness (Ew)
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184 gfop Calculate the frequency of optimal codons (Fop)
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185 gscs Calculates the scaled chi-square
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186 gwvalue Calculate the 'relative adaptiveness of each codon' (W)
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187
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188 Author(s)
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189
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190 Hidetoshi Itaya (celery@g-language.org)
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191 Institute for Advanced Biosciences, Keio University
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192 252-0882 Japan
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193
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194 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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195 Institute for Advanced Biosciences, Keio University
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196 252-0882 Japan
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197
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198 History
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199
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200 2012 - Written by Hidetoshi Itaya
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201 2013 - Fixed by Hidetoshi Itaya
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202
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203 Target users
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204
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205 This program is intended to be used by everyone and everything, from
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206 naive users to embedded scripts.
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207
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208 Comments
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209
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210 None.
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211
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