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1 goligomercounter
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2 Function
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3
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4 Counts the number of given oligomers in a sequence
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5
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6 Description
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7
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8 goligomercounter counts the number of oligomers in a sequence (by windows
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9 optionally). Oligomer can be specified using degenerate nucleotide alphabet,
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10 or by regular expressions. k-mers can be counted by specifying the "-length"
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11 qualifier.
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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 goligomercounter
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31
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32 % goligomercounter refseqn:NC_000913 atgcatgc
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33 Counts the number of given oligomers in a sequence
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34 Program compseq output file [nc_000913.goligomercounter]:
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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 count (Any string)
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45 [-outfile] outfile [*.goligomercounter] 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 -window integer [0] Int window size (Any integer value)
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51 -[no]accid boolean [Y] Include to use sequence accession ID as
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52 query
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53
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54 Associated qualifiers:
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55
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56 "-sequence" associated qualifiers
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57 -sbegin1 integer Start of each sequence to be used
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58 -send1 integer End of each sequence to be used
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59 -sreverse1 boolean Reverse (if DNA)
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60 -sask1 boolean Ask for begin/end/reverse
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61 -snucleotide1 boolean Sequence is nucleotide
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62 -sprotein1 boolean Sequence is protein
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63 -slower1 boolean Make lower case
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64 -supper1 boolean Make upper case
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65 -scircular1 boolean Sequence is circular
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66 -sformat1 string Input sequence format
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67 -iquery1 string Input query fields or ID list
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68 -ioffset1 integer Input start position offset
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69 -sdbname1 string Database name
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70 -sid1 string Entryname
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71 -ufo1 string UFO features
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72 -fformat1 string Features format
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73 -fopenfile1 string Features file name
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74
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75 "-outfile" associated qualifiers
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76 -odirectory3 string Output directory
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77
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78 General qualifiers:
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79 -auto boolean Turn off prompts
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80 -stdout boolean Write first file to standard output
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81 -filter boolean Read first file from standard input, write
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82 first file to standard output
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83 -options boolean Prompt for standard and additional values
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84 -debug boolean Write debug output to program.dbg
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85 -verbose boolean Report some/full command line options
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86 -help boolean Report command line options and exit. More
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87 information on associated and general
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88 qualifiers can be found with -help -verbose
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89 -warning boolean Report warnings
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90 -error boolean Report errors
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91 -fatal boolean Report fatal errors
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92 -die boolean Report dying program messages
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93 -version boolean Report version number and exit
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94
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95 Input file format
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96
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97 The database definitions for following commands are available at
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98 http://soap.g-language.org/kbws/embossrc
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99
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100 goligomercounter reads one or more nucleotide sequences.
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101
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102 Output file format
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103
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104 The output from goligomercounter is to a plain text file.
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105
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106 File: nc_000913.goligomercounter
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107
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108 Sequence: NC_000913 Oligomer: atgcatgc Number: 27
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109
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110
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111 Data files
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112
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113 None.
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114
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115 Notes
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116
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117 None.
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118
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119 References
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120
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121 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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122 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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123 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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124
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125 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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126 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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127 31, 7.
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128
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129 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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130 Analysis Environment with REST and SOAP Web Service Interfaces,
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131 Nucleic Acids Res., 38, W700-W705.
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132
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133 Warnings
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134
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135 None.
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136
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137 Diagnostic Error Messages
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138
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139 None.
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140
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141 Exit status
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142
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143 It always exits with a status of 0.
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144
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145 Known bugs
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146
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147 None.
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148
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149 See also
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150
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151 gkmertable Create an image showing all k-mer abundance within a
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152 sequence
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153 gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
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154 goligomersearch Searches oligomers in given sequence
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155 gsignature Calculate oligonucleotide usage (genomic signature)
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156
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157 Author(s)
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158
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159 Hidetoshi Itaya (celery@g-language.org)
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160 Institute for Advanced Biosciences, Keio University
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161 252-0882 Japan
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162
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163 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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164 Institute for Advanced Biosciences, Keio University
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165 252-0882 Japan
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166
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167 History
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168
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169 2012 - Written by Hidetoshi Itaya
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170 2013 - Fixed by Hidetoshi Itaya
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171
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172 Target users
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173
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174 This program is intended to be used by everyone and everything, from
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175 naive users to embedded scripts.
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176
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177 Comments
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178
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179 None.
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180
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