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1 gdeltaenc
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2 Function
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3
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4 Calculate the codon usage bias related to translation optimization
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5 (delta ENC)
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6
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7 Description
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8
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9 gdeltaenc calculates the codon usage bias related to translation
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10 optimization (delta ENC) described in Rocha (2004). The basic idea is to
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11 calculate the Effective Number of Codons (ENC) for highly-expressed genes
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12 (ribosomal genes) and weakly-expressed genes (all genes), and taking the
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13 relative difference between them. ENC assigns a gene a number between 20 to
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14 61 where 20 indicates that one codon is used for each aminoacid and 61
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15 indicates that each codon is used equally throughout the protein sequence.
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16
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17 ENC is calculated as follows:
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18
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19 G-language SOAP service is provided by the
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20 Institute for Advanced Biosciences, Keio University.
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21 The original web service is located at the following URL:
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22
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23 http://www.g-language.org/wiki/soap
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24
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25 WSDL(RPC/Encoded) file is located at:
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26
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27 http://soap.g-language.org/g-language.wsdl
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28
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29 Documentation on G-language Genome Analysis Environment methods are
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30 provided at the Document Center
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31
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32 http://ws.g-language.org/gdoc/
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33
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34 Usage
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35
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36 Here is a sample session with gdeltaenc
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37
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38 % gdeltaenc refseqn:NC_000913
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39 Calculate the codon usage bias related to translation optimization (delta
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40 ENC)
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41 Program compseq output file [nc_000913.gdeltaenc]:
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42
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43 Go to the input files for this example
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44 Go to the output files for this example
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45
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46 Command line arguments
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47
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48 Standard (Mandatory) qualifiers:
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49 [-sequence] seqall Nucleotide sequence(s) filename and optional
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50 format, or reference (input USA)
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51 [-outfile] outfile [*.gdeltaenc] Program compseq output file
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52
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53 Additional (Optional) qualifiers: (none)
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54 Advanced (Unprompted) qualifiers:
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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 gdeltaenc 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 gdeltaenc is to a plain text file.
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109
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110 File: nc_000913.gdeltaenc
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111
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112 Sequence: NC_000913 DELTA-ENC 0.255663430420712
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113
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114
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115 Data files
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116
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117 None.
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118
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119 Notes
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120
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121 None.
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122
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123 References
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124
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125 Rocha EPC (2004) Codon usage bias from tRNA's point of view: Redundancy,
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126 specialization, and efficient decoding for translation optimization,
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127 Genome Research, 14(11):2279-2286
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128
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129 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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130 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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131 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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132
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133 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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134 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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135 31, 7.
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136
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137 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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138 Analysis Environment with REST and SOAP Web Service Interfaces,
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139 Nucleic Acids Res., 38, W700-W705.
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140
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141 Warnings
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142
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143 None.
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144
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145 Diagnostic Error Messages
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146
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147 None.
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148
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149 Exit status
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150
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151 It always exits with a status of 0.
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152
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153 Known bugs
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154
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155 None.
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156
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157 See also
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158
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159 gcbi Calculates the codon bias index (CBI)
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160 gicdi Calculates the intrinsic codon deviation index (ICDI)
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161 gsvalue Calculate the strength of selected codon usage bias (S)
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162
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163 Author(s)
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164
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165 Hidetoshi Itaya (celery@g-language.org)
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166 Institute for Advanced Biosciences, Keio University
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167 252-0882 Japan
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168
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169 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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170 Institute for Advanced Biosciences, Keio University
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171 252-0882 Japan
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172
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173 History
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174
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175 2012 - Written by Hidetoshi Itaya
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176 2013 - Fixed by Hidetoshi Itaya
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177
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178 Target users
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179
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180 This program is intended to be used by everyone and everything, from
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181 naive users to embedded scripts.
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182
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183 Comments
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184
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185 None.
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186
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