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1 gbaserelativeentropy
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2 Function
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3
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4 Calculates and graphs the sequence conservation using Kullback-Leibler
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5
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6 Description
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7
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8 This function calculates and graphs the sequence conservation in regions
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9 around the start/stop codons using Kullback-Leibler divergence (relative
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10 entropy). In realistic conditions, as background nucleotide composition
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11 (e.g. G+C content) varies among species. Kullback-Leibler divergence
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12 calculates the entropy with reduced background noise.
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13
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14 The relative entropy H at position i with distribution P(i) is calculated
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15 as follows:
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16 H(P(i)||pi) = sum(P(i,j) * log(2, P(i,j)/pi(j)))
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17
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18 G-language SOAP service is provided by the
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19 Institute for Advanced Biosciences, Keio University.
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20 The original web service is located at the following URL:
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21
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22 http://www.g-language.org/wiki/soap
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23
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24 WSDL(RPC/Encoded) file is located at:
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25
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26 http://soap.g-language.org/g-language.wsdl
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27
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28 Documentation on G-language Genome Analysis Environment methods are
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29 provided at the Document Center
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30
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31 http://ws.g-language.org/gdoc/
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32
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33 Usage
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34
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35 Here is a sample session with gbaserelativeentropy
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36
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37 % gbaserelativeentropy refseqn:NC_000913
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38 Calculates and graphs the sequence conservation using Kullback-Leibler
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39 divergence (relative entropy)
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40 Program compseq output file (optional) [nc_000913.gbaserelativeentropy]:
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41
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42 Go to the input files for this example
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43 Go to the output files for this example
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44
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45 Example 2
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46
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47 % gbaserelativeentropy refseqn:NC_000913 -plot -graph png
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48 Calculates and graphs the sequence conservation using Kullback-Leibler
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49 divergence (relative entropy)
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50 Created gbaserelativeentropy.1.png
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51
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52 Go to the input files for this example
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53 Go to the output files for this example
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54
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55 Command line arguments
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56
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57 Calculates and graphs the sequence conservation using Kullback-Leibler
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58 divergence (relative entropy)
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59 Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1
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60
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61 Standard (Mandatory) qualifiers (* if not always prompted):
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62 [-sequence] seqall Nucleotide sequence(s) filename and optional
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63 format, or reference (input USA)
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64 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
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65 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
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66 tek, tekt, none, data, xterm, png, gif, svg)
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67 * -outfile outfile [*.gbaserelativeentropy] Program compseq
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68 output file (optional)
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69
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70 Additional (Optional) qualifiers: (none)
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71 Advanced (Unprompted) qualifiers:
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72 -position selection [start] Either 'start' (around start codon)
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73 or 'end' (around stop codon) to create the
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74 PWM
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75 -patlen integer [3] Length of oligomer to count (Any integer
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76 value)
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77 -upstream integer [30] Length upstream of specified position
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78 to create PWM (Any integer value)
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79 -downstream integer [30] Length downstream of specified position
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80 to create PWM (Any integer value)
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81 -[no]accid boolean [Y] Include to use sequence accession ID as
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82 query
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83 -plot toggle [N] Include to plot result
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84
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85 Associated qualifiers:
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86
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87 "-sequence" associated qualifiers
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88 -sbegin1 integer Start of each sequence to be used
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89 -send1 integer End of each sequence to be used
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90 -sreverse1 boolean Reverse (if DNA)
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91 -sask1 boolean Ask for begin/end/reverse
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92 -snucleotide1 boolean Sequence is nucleotide
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93 -sprotein1 boolean Sequence is protein
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94 -slower1 boolean Make lower case
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95 -supper1 boolean Make upper case
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96 -scircular1 boolean Sequence is circular
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97 -sformat1 string Input sequence format
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98 -iquery1 string Input query fields or ID list
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99 -ioffset1 integer Input start position offset
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100 -sdbname1 string Database name
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101 -sid1 string Entryname
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102 -ufo1 string UFO features
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103 -fformat1 string Features format
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104 -fopenfile1 string Features file name
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105
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106 "-graph" associated qualifiers
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107 -gprompt boolean Graph prompting
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108 -gdesc string Graph description
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109 -gtitle string Graph title
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110 -gsubtitle string Graph subtitle
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111 -gxtitle string Graph x axis title
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112 -gytitle string Graph y axis title
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113 -goutfile string Output file for non interactive displays
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114 -gdirectory string Output directory
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115
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116 "-outfile" associated qualifiers
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117 -odirectory string Output directory
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118
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119 General qualifiers:
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120 -auto boolean Turn off prompts
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121 -stdout boolean Write first file to standard output
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122 -filter boolean Read first file from standard input, write
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123 first file to standard output
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124 -options boolean Prompt for standard and additional values
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125 -debug boolean Write debug output to program.dbg
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126 -verbose boolean Report some/full command line options
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127 -help boolean Report command line options and exit. More
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128 information on associated and general
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129 qualifiers can be found with -help -verbose
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130 -warning boolean Report warnings
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131 -error boolean Report errors
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132 -fatal boolean Report fatal errors
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133 -die boolean Report dying program messages
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134 -version boolean Report version number and exit
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135
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136 Input file format
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137
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138 The database definitions for following commands are available at
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139 http://soap.g-language.org/kbws/embossrc
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140
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141 gbaserelativeentropy reads one or more nucleotide sequences.
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142
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143 Output file format
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144
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145 The output from gbaserelativeentropy is to a plain text file or the
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146 EMBOSS graphics device.
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147
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148 File: nc_000913.gbaserelativeentropy
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149
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150 Sequence: NC_000913
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151 -30,-0.46682
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152 -29,-0.46265
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153 -28,-0.45732
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154 -27,-0.45704
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155 -26,-0.44692
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156 -25,-0.44396
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157 -24,-0.43528
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158 -23,-0.43419
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159 -22,-0.42518
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160
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161 [Part of this file has been deleted for brevity]
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162
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163 21,-0.40010
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164 22,-0.41772
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165 23,-0.42503
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166 24,-0.39675
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167 25,-0.43091
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168 26,-0.43196
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169 27,-0.40576
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170 28,-0.43387
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171 29,-0.41228
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172 30,-0.38869
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173
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174
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175 Data files
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176
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177 None.
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178
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179 Notes
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180
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181 None.
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182
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183 References
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184
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185 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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186 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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187 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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188
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189 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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190 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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191 31, 7.
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192
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193 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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194 Analysis Environment with REST and SOAP Web Service Interfaces,
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195 Nucleic Acids Res., 38, W700-W705.
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196
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197 Warnings
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198
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199 None.
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200
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201 Diagnostic Error Messages
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202
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203 None.
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204
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205 Exit status
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206
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207 It always exits with a status of 0.
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208
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209 Known bugs
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210
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211 None.
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212
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213 See also
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214
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215 gbase_entropy Calculates and graphs the sequence conservation
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216 using Shanon uncertainty (entropy)
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217 gbase_information_content Calculates and graphs the sequence conservation
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218 using information content
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219
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220 Author(s)
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221
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222 Hidetoshi Itaya (celery@g-language.org)
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223 Institute for Advanced Biosciences, Keio University
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224 252-0882 Japan
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225
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226 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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227 Institute for Advanced Biosciences, Keio University
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228 252-0882 Japan
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229
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230 History
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231
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232 2012 - Written by Hidetoshi Itaya
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233 2013 - Fixed by Hidetoshi Itaya
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234
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235 Target users
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236
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237 This program is intended to be used by everyone and everything, from
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238 naive users to embedded scripts.
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239
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240 Comments
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241
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242 None.
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243
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