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1 goligomersearch
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2 Function
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3
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4 Searches oligomers in given sequence
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5
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6 Description
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7
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8 goligomersearch searches for the given oligomer in given sequence. Oligomer
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9 can be specified using degenerate nucleotide alphabet, or by regular
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10 expressions. Performance is optimized for fast searching.
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11 This method changes the returning value according to the given options.
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12
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13 G-language SOAP service is provided by the
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14 Institute for Advanced Biosciences, Keio University.
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15 The original web service is located at the following URL:
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16
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17 http://www.g-language.org/wiki/soap
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18
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19 WSDL(RPC/Encoded) file is located at:
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20
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21 http://soap.g-language.org/g-language.wsdl
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22
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23 Documentation on G-language Genome Analysis Environment methods are
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24 provided at the Document Center
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25
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26 http://ws.g-language.org/gdoc/
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27
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28 Usage
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29
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30 Here is a sample session with goligomersearch
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31
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32 % goligomersearch refseqn:NC_000913 atgcatgc
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33 Searches oligomers in given sequence
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34 Program compseq output file [nc_000913.goligomersearch]:
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35
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36 Go to the input files for this example
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37 Go to the output files for this example
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38
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39 Command line arguments
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40
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41 Standard (Mandatory) qualifiers:
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42 [-sequence] seqall Nucleotide sequence(s) filename and optional
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43 format, or reference (input USA)
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44 [-oligomer] string Oligomer to search (Any string)
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45 [-outfile] outfile [*.goligomersearch] Program compseq output
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46 file
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47
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48 Additional (Optional) qualifiers: (none)
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49 Advanced (Unprompted) qualifiers:
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50 -return selection [position] 'position' to return list of
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51 positions where oligomers are found, 'oligo'
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52 to return list of oligomers found ordered
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53 by positions, 'both' to return a hash with
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54 positions as keys and oligomers as values,
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55 'distribution' to return four values about
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56 the distribution of given oligomer
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57 -[no]accid boolean [Y] Include to use sequence accession ID as
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58 query
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59
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60 Associated qualifiers:
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61
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62 "-sequence" associated qualifiers
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63 -sbegin1 integer Start of each sequence to be used
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64 -send1 integer End of each sequence to be used
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65 -sreverse1 boolean Reverse (if DNA)
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66 -sask1 boolean Ask for begin/end/reverse
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67 -snucleotide1 boolean Sequence is nucleotide
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68 -sprotein1 boolean Sequence is protein
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69 -slower1 boolean Make lower case
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70 -supper1 boolean Make upper case
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71 -scircular1 boolean Sequence is circular
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72 -sformat1 string Input sequence format
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73 -iquery1 string Input query fields or ID list
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74 -ioffset1 integer Input start position offset
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75 -sdbname1 string Database name
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76 -sid1 string Entryname
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77 -ufo1 string UFO features
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78 -fformat1 string Features format
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79 -fopenfile1 string Features file name
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80
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81 "-outfile" associated qualifiers
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82 -odirectory3 string Output directory
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83
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84 General qualifiers:
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85 -auto boolean Turn off prompts
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86 -stdout boolean Write first file to standard output
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87 -filter boolean Read first file from standard input, write
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88 first file to standard output
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89 -options boolean Prompt for standard and additional values
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90 -debug boolean Write debug output to program.dbg
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91 -verbose boolean Report some/full command line options
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92 -help boolean Report command line options and exit. More
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93 information on associated and general
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94 qualifiers can be found with -help -verbose
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95 -warning boolean Report warnings
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96 -error boolean Report errors
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97 -fatal boolean Report fatal errors
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98 -die boolean Report dying program messages
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99 -version boolean Report version number and exit
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100
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101 Input file format
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102
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103 The database definitions for following commands are available at
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104 http://soap.g-language.org/kbws/embossrc
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105
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106 goligomersearch reads one or more nucleotide sequences.
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107
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108 Output file format
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109
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110 The output from goligomersearch is to a plain text file.
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111
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112 File: nc_000913.goligomersearch
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113
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114 Sequence: NC_000913 Oligomer: atgcatgc Return: 147018,366819,653138,863326,1288615,1627117,2111200,2246695,2697278,2750962,2826906,2882353,2998362,3022134,3346029,3477018,3629113,3842819,3958304,3982183,4013480,4285578,4474663,4484501,4499080,4604562,4638391
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115
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116
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117 Data files
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118
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119 None.
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120
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121 Notes
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122
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123 None.
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124
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125 References
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126
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127 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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128 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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129 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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130
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131 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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132 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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133 31, 7.
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134
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135 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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136 Analysis Environment with REST and SOAP Web Service Interfaces,
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137 Nucleic Acids Res., 38, W700-W705.
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138
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139 Warnings
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140
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141 None.
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142
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143 Diagnostic Error Messages
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144
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145 None.
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146
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147 Exit status
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148
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149 It always exits with a status of 0.
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150
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151 Known bugs
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152
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153 None.
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154
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155 See also
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156
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157 gkmertable Create an image showing all k-mer abundance within a
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158 sequence
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159 gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
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160 goligomercounter Counts the number of given oligomers in a sequence
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161 gsignature Calculate oligonucleotide usage (genomic signature)
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162
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163 Author(s)
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164
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165 Hidetoshi Itaya (celery@g-language.org)
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166 Institute for Advanced Biosciences, Keio University
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167 252-0882 Japan
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168
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169 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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170 Institute for Advanced Biosciences, Keio University
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171 252-0882 Japan
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172
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173 History
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174
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175 2012 - Written by Hidetoshi Itaya
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176 2013 - Fixed by Hidetoshi Itaya
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177
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178 Target users
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179
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180 This program is intended to be used by everyone and everything, from
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181 naive users to embedded scripts.
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182
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183 Comments
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184
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185 None.
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186
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