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1 gcodoncompiler
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2 Function
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3
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4 Calculate various kinds of amino acid and codon usage data
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5
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6 Description
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7
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8 gcodoncompiler calculates various kinds of amino acid and codon usage data.
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9 The following values are calculable:
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10 A0: Absolute amino acid frequency
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11 A1: Relative amino acid frequency
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12 C0: Absolute codon frequency
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13 C1: Relative codon frequency in a complete sequence
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14 C2: Relative codon frequency in each amino acid
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15 C3: Relative synonymous codon usage
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16 C4: Relative adaptiveness
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17 C5: Maximum or minor codon
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18
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19 For amino acids unpresent in a gene, C2-C3 does not calculate the values.
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20 By using R* in place, such values are hypothesized that alternative
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21 synonymous codons are used with equal frequency.
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22
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23 G-language SOAP service is provided by the
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24 Institute for Advanced Biosciences, Keio University.
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25 The original web service is located at the following URL:
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26
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27 http://www.g-language.org/wiki/soap
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28
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29 WSDL(RPC/Encoded) file is located at:
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30
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31 http://soap.g-language.org/g-language.wsdl
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32
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33 Documentation on G-language Genome Analysis Environment methods are
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34 provided at the Document Center
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35
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36 http://ws.g-language.org/gdoc/
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37
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38 Usage
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39
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40 Here is a sample session with gcodoncompiler
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41
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42 % gcodoncompiler refseqn:NC_000913
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43 Calculate various kinds of amino acid and codon usage data
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44 Codon usage output file [nc_000913.gcodoncompiler]:
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45
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46 Go to the input files for this example
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47 Go to the output files for this example
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48
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49 Command line arguments
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50
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51 Standard (Mandatory) qualifiers:
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52 [-sequence] seqall Nucleotide sequence(s) filename and optional
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53 format, or reference (input USA)
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54 [-outfile] outfile [*.gcodoncompiler] Codon usage output file
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55
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56 Additional (Optional) qualifiers: (none)
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57 Advanced (Unprompted) qualifiers:
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58 -translate boolean [N] Include to translate using standard
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59 codon table
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60 -startcodon boolean [N] Include to include start codon
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61 -stopcodon boolean [N] Include to include stop codon
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62 -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
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63 expression to delete key (i.e. amino acids
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64 and nucleotides) (Any string)
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65 -data menu [R0] Kinds of codon usage data. R*
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66 hypothesizes amino acids which are not
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67 present in the gene (Values: A0 (Absolute
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68 amino acid frequency ('AA')); A1 (Relative
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69 amino acid frequency ('RAAU')); C0 (Absolute
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70 codon frequency ('AF')); C1 (Relative codon
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71 frequency in a complete sequence); C2
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72 (Relative codon frequency in each amino acid
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73 ('RF')); C3 (Relative synonymous codon
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74 usage ('RSCU')); C4 (Relative adaptiveness);
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75 i.e., ratio to maximum of minor codon ('W')
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76 C5 (Maximum (1) or minor (0) codon); R0
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77 (Absolute codon frequency ('AF')); R1
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78 (Relative codon frequency in a complete
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79 sequence); R2 (Relative codon frequency in
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80 each amino acid ('RF')); R3 (Relative
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81 synonymous codon usage ('RSCU')); R4
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82 (Relative adaptiveness); i.e., ratio to
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83 maximum of minor codon ('W') R5 (Maximum (1)
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84 or minor (0) codon))
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85 -[no]accid boolean [Y] Include to use sequence accession ID as
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86 query
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87
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88 Associated qualifiers:
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89
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90 "-sequence" associated qualifiers
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91 -sbegin1 integer Start of each sequence to be used
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92 -send1 integer End of each sequence to be used
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93 -sreverse1 boolean Reverse (if DNA)
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94 -sask1 boolean Ask for begin/end/reverse
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95 -snucleotide1 boolean Sequence is nucleotide
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96 -sprotein1 boolean Sequence is protein
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97 -slower1 boolean Make lower case
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98 -supper1 boolean Make upper case
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99 -scircular1 boolean Sequence is circular
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100 -sformat1 string Input sequence format
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101 -iquery1 string Input query fields or ID list
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102 -ioffset1 integer Input start position offset
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103 -sdbname1 string Database name
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104 -sid1 string Entryname
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105 -ufo1 string UFO features
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106 -fformat1 string Features format
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107 -fopenfile1 string Features file name
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108
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109 "-outfile" associated qualifiers
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110 -odirectory2 string Output directory
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111
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112 General qualifiers:
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113 -auto boolean Turn off prompts
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114 -stdout boolean Write first file to standard output
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115 -filter boolean Read first file from standard input, write
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116 first file to standard output
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117 -options boolean Prompt for standard and additional values
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118 -debug boolean Write debug output to program.dbg
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119 -verbose boolean Report some/full command line options
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120 -help boolean Report command line options and exit. More
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121 information on associated and general
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122 qualifiers can be found with -help -verbose
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123 -warning boolean Report warnings
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124 -error boolean Report errors
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125 -fatal boolean Report fatal errors
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126 -die boolean Report dying program messages
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127 -version boolean Report version number and exit
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128
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129 Input file format
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130
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131 The database definitions for following commands are available at
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132 http://soap.g-language.org/kbws/embossrc
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133
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134 gcodoncompiler reads one or more nucleotide sequences.
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135
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136 Output file format
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137
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138 The output from gcodoncompiler is to a plain text file.
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139
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140 File: nc_000913.gcodoncompiler
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141
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142 Sequence: NC_000913
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143 Agca,Agcc,Agcg,Agct,Ctgc,Ctgt,Dgac,Dgat,Egaa,Egag,Fttc,Fttt,Ggga,Gggc,Gggg,Gggt,Hcac,Hcat,Iata,Iatc,Iatt,Kaaa,Kaag,Lcta,Lctc,Lctg,Lctt,Ltta,Lttg,Matg,Naac,Naat,Pcca,Pccc,Pccg,Pcct,Qcaa,Qcag,Raga,Ragg,Rcga,Rcgc,Rcgg,Rcgt,Sagc,Sagt,Stca,Stcc,Stcg,Stct,Taca,Tacc,Tacg,Tact,Utga,Vgta,Vgtc,Vgtg,Vgtt,Wtgg,Ytac,Ytat,locus_tag
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144 26551,33911,44924,20010,8486,6707,25234,42161,52362,23474,21841,29334,10226,39395,14472,32678,12830,16952,5356,33359,40221,44272,13398,5079,14709,70441,14410,18097,17936,32971,28329,22786,11063,7142,30994,9130,20216,38169,2495,1366,4529,29308,6991,27864,21132,11323,9159,11332,11759,10992,8979,31001,18989,11581,3,14337,20240,34499,24056,20071,16088,21069,
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145
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146
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147 Data files
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148
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149 None.
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150
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151 Notes
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152
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153 None.
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154
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155 References
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156
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157 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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158 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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159 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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160
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161 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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162 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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163 31, 7.
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164
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165 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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166 Analysis Environment with REST and SOAP Web Service Interfaces,
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167 Nucleic Acids Res., 38, W700-W705.
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168
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169 Warnings
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170
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171 None.
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172
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173 Diagnostic Error Messages
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174
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175 None.
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176
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177 Exit status
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178
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179 It always exits with a status of 0.
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180
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181 Known bugs
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182
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183 None.
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184
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185 See also
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186
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187 gaminoinfo Prints out basic amino acid sequence statistics
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188 gaaui Calculates various indece of amino acid usage
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189
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190 Author(s)
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191
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192 Hidetoshi Itaya (celery@g-language.org)
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193 Institute for Advanced Biosciences, Keio University
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194 252-0882 Japan
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195
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196 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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197 Institute for Advanced Biosciences, Keio University
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198 252-0882 Japan
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199
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200 History
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201
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202 2012 - Written by Hidetoshi Itaya
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203 2013 - Fixed by Hidetoshi Itaya
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204
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205 Target users
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206
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207 This program is intended to be used by everyone and everything, from
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208 naive users to embedded scripts.
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209
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210 Comments
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211
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212 None.
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213
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