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1 gbaseentropy
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2 Function
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3
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4 Calculates and graphs the sequence conservation using Shanon uncertainty
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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 Shanon uncertainty (entropy). Smaller
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10 values resemble higher conservation where the minumum value is 0 and the
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11 maximum value is 2. The entropy is typically the lowest around position 0
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12 (start/stop codon position).
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13
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14 The entropy H at position i with distribution P(i) is calculated as follows:
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15 H(P(i)) = -sum(P(i,j) * log(2,P(i,j)))
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16
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17 G-language SOAP service is provided by the
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18 Institute for Advanced Biosciences, Keio University.
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19 The original web service is located at the following URL:
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20
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21 http://www.g-language.org/wiki/soap
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22
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23 WSDL(RPC/Encoded) file is located at:
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24
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25 http://soap.g-language.org/g-language.wsdl
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26
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27 Documentation on G-language Genome Analysis Environment methods are
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28 provided at the Document Center
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29
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30 http://ws.g-language.org/gdoc/
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31
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32 Usage
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33
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34 Here is a sample session with gbaseentropy
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35
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36 % gbaseentropy refseqn:NC_000913
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37 Calculates and graphs the sequence conservation using Shanon uncertainty
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38 (entropy)
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39 Program compseq output file (optional) [nc_000913.gbaseentropy]:
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40
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41 Go to the input files for this example
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42 Go to the output files for this example
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43
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44 Example 2
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45
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46 % gbaseentropy refseqn:NC_000913 -plot -graph png
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47 Calculates and graphs the sequence conservation using Shanon uncertainty
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48 (entropy)
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49 Created gbaseentropy.1.png
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50
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51 Go to the input files for this example
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52 Go to the output files for this example
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53
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54 Command line arguments
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55
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56 Calculates and graphs the sequence conservation using Shanon uncertainty
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57 (entropy)
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58 Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1
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59
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60 Standard (Mandatory) qualifiers (* if not always prompted):
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61 [-sequence] seqall Nucleotide sequence(s) filename and optional
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62 format, or reference (input USA)
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63 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
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64 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
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65 tek, tekt, none, data, xterm, png, gif, svg)
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66 * -outfile outfile [*.gbaseentropy] Program compseq output file
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67 (optional)
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68
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69 Additional (Optional) qualifiers: (none)
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70 Advanced (Unprompted) qualifiers:
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71 -position selection [start] Either 'start' (around start codon)
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72 or 'end' (around stop codon) to create the
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73 PWM
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74 -patlen integer [3] Length of oligomer to count (Any integer
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75 value)
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76 -upstream integer [30] Length upstream of specified position
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77 to create PWM (Any integer value)
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78 -downstream integer [30] Length downstream of specified position
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79 to create PWM (Any integer value)
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80 -[no]accid boolean [Y] Include to use sequence accession ID as
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81 query
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82 -plot toggle [N] Include to plot result
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83
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84 Associated qualifiers:
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85
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86 "-sequence" associated qualifiers
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87 -sbegin1 integer Start of each sequence to be used
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88 -send1 integer End of each sequence to be used
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89 -sreverse1 boolean Reverse (if DNA)
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90 -sask1 boolean Ask for begin/end/reverse
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91 -snucleotide1 boolean Sequence is nucleotide
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92 -sprotein1 boolean Sequence is protein
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93 -slower1 boolean Make lower case
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94 -supper1 boolean Make upper case
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95 -scircular1 boolean Sequence is circular
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96 -sformat1 string Input sequence format
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97 -iquery1 string Input query fields or ID list
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98 -ioffset1 integer Input start position offset
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99 -sdbname1 string Database name
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100 -sid1 string Entryname
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101 -ufo1 string UFO features
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102 -fformat1 string Features format
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103 -fopenfile1 string Features file name
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104
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105 "-graph" associated qualifiers
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106 -gprompt boolean Graph prompting
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107 -gdesc string Graph description
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108 -gtitle string Graph title
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109 -gsubtitle string Graph subtitle
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110 -gxtitle string Graph x axis title
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111 -gytitle string Graph y axis title
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112 -goutfile string Output file for non interactive displays
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113 -gdirectory string Output directory
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114
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115 "-outfile" associated qualifiers
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116 -odirectory string Output directory
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117
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118 General qualifiers:
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119 -auto boolean Turn off prompts
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120 -stdout boolean Write first file to standard output
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121 -filter boolean Read first file from standard input, write
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122 first file to standard output
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123 -options boolean Prompt for standard and additional values
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124 -debug boolean Write debug output to program.dbg
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125 -verbose boolean Report some/full command line options
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126 -help boolean Report command line options and exit. More
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127 information on associated and general
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128 qualifiers can be found with -help -verbose
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129 -warning boolean Report warnings
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130 -error boolean Report errors
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131 -fatal boolean Report fatal errors
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132 -die boolean Report dying program messages
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133 -version boolean Report version number and exit
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134
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135 Input file format
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136
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137 The database definitions for following commands are available at
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138 http://soap.g-language.org/kbws/embossrc
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139
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140 gbaseentropy reads one or more nucleotide sequences.
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141
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142 Output file format
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143
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144 The output from gbaseentropy is to a plain text file or the EMBOSS
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145 graphics device.
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146
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147 File: nc_000913.gbaseentropy
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148
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149 Sequence: NC_000913
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150 -30,1.98284
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151 -29,1.97873
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152 -28,1.97692
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153 -27,1.97595
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154 -26,1.97094
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155 -25,1.96777
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156 -24,1.96272
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157 -23,1.96288
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158 -22,1.95707
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159
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160 [Part of this file has been deleted for brevity]
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161
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162 21,1.93528
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163 22,1.94470
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164 23,1.95204
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165 24,1.93139
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166 25,1.95640
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167 26,1.95711
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168 27,1.93785
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169 28,1.96060
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170 29,1.94316
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171 30,1.92581
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172
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173
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174 Data files
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175
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176 None.
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177
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178 Notes
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179
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180 None.
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181
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182 References
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183
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184 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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185 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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186 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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187
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188 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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189 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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190 31, 7.
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191
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192 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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193 Analysis Environment with REST and SOAP Web Service Interfaces,
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194 Nucleic Acids Res., 38, W700-W705.
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195
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196 Warnings
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197
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198 None.
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199
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200 Diagnostic Error Messages
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201
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202 None.
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203
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204 Exit status
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205
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206 It always exits with a status of 0.
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207
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208 Known bugs
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209
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210 None.
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211
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212 See also
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213
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214 gbaseinformationcontent Calculates and graphs the sequence conservation
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215 using information content
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216 gbaserelativeentropy Calculates and graphs the sequence conservation
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217 using Kullback-Leibler divergence (relative
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218 entropy)
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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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