annotate GEMBASSY-1.0.3/doc/text/gbasezvalue.txt @ 0:8300eb051bea draft

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author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 gbasezvalue
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2 Function
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3
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4 Extracts conserved oligomers per position using Z-score
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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 extracts conserved oligomers per position using
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9 Z-score, in regions around the start/stop codons. The oligomers are returned
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10 in ranking order up to "-limit" number.
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11
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12 The Z-score for mean m and standard error SE is calculated as follows:
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13 z = (x - m) / SE
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14 where SE for standard deviation s and number of samples s is as follows:
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15 SE = s/sqrt(n)
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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 gbasezvalue
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35
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36 % gbasezvalue refseqn:NC_000913
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37 Extracts conserved oligomers per position using Z-score
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38 Program compseq output file (optional) [nc_000913.gbasezvalue]:
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39
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40 Go to the input files for this example
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41 Go to the output files for this example
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42
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43 Command line arguments
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44
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45 Standard (Mandatory) qualifiers:
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46 [-sequence] seqall Nucleotide sequence(s) filename and optional
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47 format, or reference (input USA)
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48 [-outfile] outfile [*.gbasezvalue] Program compseq output file
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49 (optional)
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50
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51 Additional (Optional) qualifiers: (none)
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52 Advanced (Unprompted) qualifiers:
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53 -limit integer [5] Rank threshold for showing the conserved
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54 oligomer (Any integer value)
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55 -position selection [start] Either 'start' (around start codon)
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56 or 'end' (around stop codon) to create the
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57 PWM
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58 -patlen integer [3] Length of oligomer to count (Any integer
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59 value)
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60 -upstream integer [30] Length upstream of specified position
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61 to create PWM (Any integer value)
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62 -downstream integer [30] Length downstream of specified position
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63 to create PWM (Any integer value)
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64 -[no]accid boolean [Y] Include to use sequence accession ID as
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65 query
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66
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67 Associated qualifiers:
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68
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69 "-sequence" associated qualifiers
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70 -sbegin1 integer Start of each sequence to be used
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71 -send1 integer End of each sequence to be used
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72 -sreverse1 boolean Reverse (if DNA)
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73 -sask1 boolean Ask for begin/end/reverse
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74 -snucleotide1 boolean Sequence is nucleotide
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75 -sprotein1 boolean Sequence is protein
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76 -slower1 boolean Make lower case
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77 -supper1 boolean Make upper case
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78 -scircular1 boolean Sequence is circular
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79 -sformat1 string Input sequence format
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80 -iquery1 string Input query fields or ID list
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81 -ioffset1 integer Input start position offset
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82 -sdbname1 string Database name
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83 -sid1 string Entryname
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84 -ufo1 string UFO features
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85 -fformat1 string Features format
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86 -fopenfile1 string Features file name
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87
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88 "-outfile" associated qualifiers
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89 -odirectory2 string Output directory
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90
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91 General qualifiers:
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92 -auto boolean Turn off prompts
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93 -stdout boolean Write first file to standard output
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94 -filter boolean Read first file from standard input, write
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95 first file to standard output
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96 -options boolean Prompt for standard and additional values
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97 -debug boolean Write debug output to program.dbg
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98 -verbose boolean Report some/full command line options
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99 -help boolean Report command line options and exit. More
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100 information on associated and general
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101 qualifiers can be found with -help -verbose
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102 -warning boolean Report warnings
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103 -error boolean Report errors
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104 -fatal boolean Report fatal errors
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105 -die boolean Report dying program messages
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106 -version boolean Report version number and exit
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107
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108 Input file format
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109
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110 The database definitions for following commands are available at
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111 http://soap.g-language.org/kbws/embossrc
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112
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113 gbasezvalue reads one or more nucleotide sequences.
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114
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115 Output file format
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116
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117 The output from gbasezvalue is to a plain text file.
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118
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119 File: nc_000913.gbasezvalue
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120
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121 Sequence: NC_000913
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122 position:-30,1,taa,-0.76525
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123 2,aga,-0.79101
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124 3,tta,-1.14174
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125 4,cta,-1.18831
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126 5,aat,-1.86652
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127 position:-29,1,cta,-0.18368
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128 2,aat,-0.71851
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129 3,gac,-1.26182
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130 4,taa,-1.39455
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131
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132 [Part of this file has been deleted for brevity]
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133
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134 position:29,1,gct,1.66288
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135 2,act,1.26637
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136 3,tat,0.66721
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137 4,cct,-0.43158
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138 5,tgt,-0.59254
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139 position:30,1,ctg,3.12072
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140 2,att,0.04193
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141 3,ctc,-0.12416
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142 4,cta,-0.38461
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143 5,tta,-0.76413
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144
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145
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146 Data files
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147
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148 None.
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149
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150 Notes
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151
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152 None.
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153
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154 References
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155
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156 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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157 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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158 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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159
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160 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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161 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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162 31, 7.
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163
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164 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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165 Analysis Environment with REST and SOAP Web Service Interfaces,
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166 Nucleic Acids Res., 38, W700-W705.
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167
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168 Warnings
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169
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170 None.
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171
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172 Diagnostic Error Messages
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173
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174 None.
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175
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176 Exit status
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177
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178 It always exits with a status of 0.
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179
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180 Known bugs
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181
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182 None.
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183
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184 See also
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185
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186 gbasecounter Creates a position weight matrix of oligomers around start
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187 codon
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188 gviewcds Displays a graph of nucleotide contents around start and stop
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189 codons
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190
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191 Author(s)
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192
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193 Hidetoshi Itaya (celery@g-language.org)
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194 Institute for Advanced Biosciences, Keio University
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195 252-0882 Japan
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196
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197 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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198 Institute for Advanced Biosciences, Keio University
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199 252-0882 Japan
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200
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201 History
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202
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203 2012 - Written by Hidetoshi Itaya
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204 2013 - Fixed by Hidetoshi Itaya
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205
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206 Target users
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207
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208 This program is intended to be used by everyone and everything, from
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209 naive users to embedded scripts.
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210
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211 Comments
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212
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213 None.
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214