Mercurial > repos > ktnyt > gembassy

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

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Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 gconsensusz
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2 Function
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3
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4 Calculate consensus in given array of sequences
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5
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6 Description
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7
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8 gconsensusz calculates the consensus of given list of sequences, using
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9 Z-score. The Z-score will show higher values when the sequences are biased
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10 to a single character within the list.
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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 gconsensusz
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35
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36 % gconsensusz consensus.fasta
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37 Calculate consensus in given array of sequences
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38 Program compseq output file (optional) [rs_000000.gconsensusz]:
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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 Example 2
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44
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45 % gconsensusz consensus.fasta -plot -graph png
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46 Calculate consensus in given array of sequences
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47 Created gconsensusz.1.png
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48
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49 Go to the input files for this example
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50 Go to the output files for this example
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51
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52 Command line arguments
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53
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54 Standard (Mandatory) qualifiers (* if not always prompted):
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55 [-sequence] seqall Nucleotide sequence(s) filename and optional
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56 format, or reference (input USA)
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57 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
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58 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
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59 tek, tekt, none, data, xterm, png, gif, svg)
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60 * -outfile outfile [*.gconsensusz] Program compseq output file
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61 (optional)
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62
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63 Additional (Optional) qualifiers: (none)
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64 Advanced (Unprompted) qualifiers:
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65 -high integer [1] Z value greater than which is
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66 significant (Any integer value)
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67 -low float [0.2] Z value less than which is
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68 insignificant (Any numeric value)
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69 -plot toggle [N] Include to plot result
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70
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71 Associated qualifiers:
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72
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73 "-sequence" associated qualifiers
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74 -sbegin1 integer Start of each sequence to be used
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75 -send1 integer End of each sequence to be used
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76 -sreverse1 boolean Reverse (if DNA)
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77 -sask1 boolean Ask for begin/end/reverse
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78 -snucleotide1 boolean Sequence is nucleotide
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79 -sprotein1 boolean Sequence is protein
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80 -slower1 boolean Make lower case
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81 -supper1 boolean Make upper case
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82 -scircular1 boolean Sequence is circular
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83 -sformat1 string Input sequence format
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84 -iquery1 string Input query fields or ID list
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85 -ioffset1 integer Input start position offset
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86 -sdbname1 string Database name
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87 -sid1 string Entryname
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88 -ufo1 string UFO features
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89 -fformat1 string Features format
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90 -fopenfile1 string Features file name
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91
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92 "-graph" associated qualifiers
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93 -gprompt boolean Graph prompting
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94 -gdesc string Graph description
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95 -gtitle string Graph title
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96 -gsubtitle string Graph subtitle
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97 -gxtitle string Graph x axis title
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98 -gytitle string Graph y axis title
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99 -goutfile string Output file for non interactive displays
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100 -gdirectory string Output directory
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101
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102 "-outfile" associated qualifiers
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103 -odirectory string Output directory
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104
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105 General qualifiers:
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106 -auto boolean Turn off prompts
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107 -stdout boolean Write first file to standard output
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108 -filter boolean Read first file from standard input, write
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109 first file to standard output
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110 -options boolean Prompt for standard and additional values
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111 -debug boolean Write debug output to program.dbg
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112 -verbose boolean Report some/full command line options
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113 -help boolean Report command line options and exit. More
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114 information on associated and general
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115 qualifiers can be found with -help -verbose
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116 -warning boolean Report warnings
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117 -error boolean Report errors
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118 -fatal boolean Report fatal errors
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119 -die boolean Report dying program messages
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120 -version boolean Report version number and exit
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121
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122 Input file format
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123
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124 The database definitions for following commands are available at
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125 http://soap.g-language.org/kbws/embossrc
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126
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127 gconsensusz reads one or more nucleotide sequences.
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128
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129 Output file format
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130
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131 The output from gconsensusz is to a plain text file or the EMBOSS graphics device.
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132
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133 File: rs_000000.gconsensusz
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134
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135 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136
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137
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138 Data files
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139
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140 None.
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141
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142 Notes
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143
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144 None.
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145
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146 References
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147
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148 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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149 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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150 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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151
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152 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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153 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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154 31, 7.
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155
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156 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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157 Analysis Environment with REST and SOAP Web Service Interfaces,
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158 Nucleic Acids Res., 38, W700-W705.
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159
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160 Warnings
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161
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162 None.
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163
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164 Diagnostic Error Messages
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165
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166 None.
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167
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168 Exit status
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169
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170 It always exits with a status of 0.
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171
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172 Known bugs
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173
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174 None.
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175
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176 See also
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177
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178 gdistincc Calculates the distance between two loci in circular chromosomes
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179 gpalindrome Searches palindrome sequences
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180 gseqinfo Prints out basic nucleotide sequence statistics
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181
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182 Author(s)
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183
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184 Hidetoshi Itaya (celery@g-language.org)
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185 Institute for Advanced Biosciences, Keio University
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186 252-0882 Japan
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187
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188 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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189 Institute for Advanced Biosciences, Keio University
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190 252-0882 Japan
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191
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192 History
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193
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194 2012 - Written by Hidetoshi Itaya
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195 2013 - Fixed by Hidetoshi Itaya
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196
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197 Target users
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198
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199 This program is intended to be used by everyone and everything, from
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200 naive users to embedded scripts.
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201
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202 Comments
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203
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204 None.
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205