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1 gbaseinformationcontent
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2 Function
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3
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4 Calculates and graphs the sequence conservation using information content
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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 information content. Values are obtained
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10 by subtracting the entropy for each positfion from the maximum possible
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11 value (which will be 2 in the case of nucleotide sequences). Information
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12 content will show the highest value when the frequency is most biased to a
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13 single alphabet.
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14
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15 Information content I is obtained by subtracting the entropy H from the
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16 maximum uncertainty log(2,|M|):
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17 I(P(i)) = log(2,|M|) - (-sum(P(i,j) * log(2,P(i,j))))
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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 gbaseinformationcontent
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37
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38 % gbaseinformationcontent refseqn:NC_000913
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39 Calculates and graphs the sequence conservation using information content
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40 Program compseq output file (optional) [nc_000913.gbaseinformationcontent]:
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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 % gbaseinformationcontent refseqn:NC_000913 -plot -graph png
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48 Calculates and graphs the sequence conservation using information content
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49 Created gbaseinformationcontent.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 Standard (Mandatory) qualifiers (* if not always prompted):
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57 [-sequence] seqall Nucleotide sequence(s) filename and optional
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58 format, or reference (input USA)
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59 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
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60 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
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61 tek, tekt, none, data, xterm, png, gif, svg)
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62 * -outfile outfile [*.gbaseinformationcontent] Program compseq
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63 output file (optional)
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64
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65 Additional (Optional) qualifiers: (none)
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66 Advanced (Unprompted) qualifiers:
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67 -position selection [start] Either 'start' (around start codon)
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68 or 'end' (around stop codon) to create the
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69 PWM
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70 -upstream integer [30] Length upstream of specified position
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71 to create PWM (Any integer value)
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72 -downstream integer [30] Length downstream of specified position
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73 to create PWM (Any integer value)
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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 -[no]accid boolean [Y] Include to use sequence accession ID as
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77 query
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78 -plot toggle [N] Include to plot result
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79
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80 Associated qualifiers:
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81
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82 "-sequence" associated qualifiers
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83 -sbegin1 integer Start of each sequence to be used
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84 -send1 integer End of each sequence to be used
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85 -sreverse1 boolean Reverse (if DNA)
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86 -sask1 boolean Ask for begin/end/reverse
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87 -snucleotide1 boolean Sequence is nucleotide
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88 -sprotein1 boolean Sequence is protein
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89 -slower1 boolean Make lower case
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90 -supper1 boolean Make upper case
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91 -scircular1 boolean Sequence is circular
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92 -sformat1 string Input sequence format
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93 -iquery1 string Input query fields or ID list
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94 -ioffset1 integer Input start position offset
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95 -sdbname1 string Database name
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96 -sid1 string Entryname
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97 -ufo1 string UFO features
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98 -fformat1 string Features format
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99 -fopenfile1 string Features file name
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100
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101 "-graph" associated qualifiers
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102 -gprompt boolean Graph prompting
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103 -gdesc string Graph description
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104 -gtitle string Graph title
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105 -gsubtitle string Graph subtitle
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106 -gxtitle string Graph x axis title
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107 -gytitle string Graph y axis title
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108 -goutfile string Output file for non interactive displays
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109 -gdirectory string Output directory
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110
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111 "-outfile" associated qualifiers
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112 -odirectory string Output directory
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113
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114 General qualifiers:
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115 -auto boolean Turn off prompts
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116 -stdout boolean Write first file to standard output
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117 -filter boolean Read first file from standard input, write
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118 first file to standard output
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119 -options boolean Prompt for standard and additional values
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120 -debug boolean Write debug output to program.dbg
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121 -verbose boolean Report some/full command line options
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122 -help boolean Report command line options and exit. More
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123 information on associated and general
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124 qualifiers can be found with -help -verbose
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125 -warning boolean Report warnings
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126 -error boolean Report errors
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127 -fatal boolean Report fatal errors
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128 -die boolean Report dying program messages
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129 -version boolean Report version number and exit
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130
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131 Input file format
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132
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133 The database definitions for following commands are available at
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134 http://soap.g-language.org/kbws/embossrc
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135
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136 gbaseinformationcontent reads one or more nucleotide sequences.
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137
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138 Output file format
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139
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140 The output from gbaseinformationcontent is to a plain text file or the
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141 EMBOSS graphics device.
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142
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143 File: nc_000913.gbaseinformationcontent
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144
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145 Sequence: NC_000913
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146 -30,2.42457
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147 -29,2.42811
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148 -28,2.43235
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149 -27,2.43116
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150 -26,2.44278
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151 -25,2.44236
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152 -24,2.44502
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153 -23,2.46097
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154 -22,2.46588
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155
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156 [Part of this file has been deleted for brevity]
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157
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158 21,2.27547
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159 22,2.46974
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160 23,2.46342
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161 24,2.32686
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162 25,2.46245
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163 26,2.46061
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164 27,2.27664
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165 28,2.45650
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166 29,2.48206
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167 30,2.29140
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168
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169
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170 Data files
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171
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172 None.
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173
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174 Notes
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175
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176 None.
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177
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178 References
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179
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180 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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181 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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182 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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183
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184 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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185 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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186 31, 7.
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187
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188 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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189 Analysis Environment with REST and SOAP Web Service Interfaces,
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190 Nucleic Acids Res., 38, W700-W705.
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191
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192 Warnings
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193
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194 None.
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195
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196 Diagnostic Error Messages
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197
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198 None.
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199
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200 Exit status
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201
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202 It always exits with a status of 0.
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203
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204 Known bugs
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205
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206 None.
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207
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208 See also
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209
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210 gbaseentropy Calculates and graphs the sequence conservation
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211 using Shanon uncertainty (entropy)
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212 gbaserelativeentropy Calculates and graphs the sequence conservation
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213 using Kullback-Leibler divergence (relative
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214 entropy)
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215
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216 Author(s)
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217
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218 Hidetoshi Itaya (celery@g-language.org)
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219 Institute for Advanced Biosciences, Keio University
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220 252-0882 Japan
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221
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222 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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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 History
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227
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228 2012 - Written by Hidetoshi Itaya
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229 2013 - Fixed by Hidetoshi Itaya
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230
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231 Target users
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232
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233 This program is intended to be used by everyone and everything, from
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234 naive users to embedded scripts.
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235
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236 Comments
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237
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238 None.
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239
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