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1 gkmertable
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2 Function
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3
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4 Create an image showing all k-mer abundance within a sequence
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5
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6 Description
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7
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8 gkmertable creates an image showing the abundance of all k-mers
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9 (oligonucleotides of length k) in a given sequence. For example, for
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10 tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each
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11 representing an oligomer. Oligomer name and abundance is written within
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12 these boxes, and abundance is also visualized with the box color, from
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13 white (none) to black (highly frequent).
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14
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15 This k-mer table is alternatively known as the FCGR (frequency matrices
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16 extracted from Chaos Game Representation).
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17 Position of the oligomers can be recursively located as follows:
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18 For each letter in an oligomer, a box is subdivided into four quadrants,
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19 where A is upper left, T is lower right, G is upper right, and C is lower
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20 left.
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21
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22 Therefore, oligomer ATGC is in the
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23 A = upper left quadrant
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24 T = lower right within the above quadrant
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25 G = upper right within the above quadrant
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26 C = lower left within the above quadrant
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27 More detailed documentation is available at
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28 http://www.g-language.org/wiki/cgr
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29
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30 G-language SOAP service is provided by the
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31 Institute for Advanced Biosciences, Keio University.
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32 The original web service is located at the following URL:
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33
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34 http://www.g-language.org/wiki/soap
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35
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36 WSDL(RPC/Encoded) file is located at:
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37
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38 http://soap.g-language.org/g-language.wsdl
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39
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40 Documentation on G-language Genome Analysis Environment methods are
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41 provided at the Document Center
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42
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43 http://ws.g-language.org/gdoc/
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44
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45 Usage
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46
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47 Here is a sample session with gkmertable
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48
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49 % gkmertable refseqn:NC_000913
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50 Create an image showing all k-mer abundance within a sequence
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51 Created gkmertable.1.png
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52
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53 Go to the input files for this example
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54 Go to the output files for this example
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55
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56 Command line arguments
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57
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58 Standard (Mandatory) qualifiers:
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59 [-sequence] seqall Nucleotide sequence(s) filename and optional
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60 format, or reference (input USA)
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61
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62 Additional (Optional) qualifiers: (none)
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63 Advanced (Unprompted) qualifiers:
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64 -format string [png] Output file format. Dependent on
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65 'convert' command (Any string)
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66 -k integer [6] Length of oligomer (Any integer value)
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67 -goutfile string [gkmertable] Output file for non interactive
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68 displays (Any string)
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69
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70 Associated qualifiers:
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71
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72 "-sequence" associated qualifiers
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73 -sbegin1 integer Start of each sequence to be used
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74 -send1 integer End of each sequence to be used
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75 -sreverse1 boolean Reverse (if DNA)
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76 -sask1 boolean Ask for begin/end/reverse
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77 -snucleotide1 boolean Sequence is nucleotide
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78 -sprotein1 boolean Sequence is protein
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79 -slower1 boolean Make lower case
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80 -supper1 boolean Make upper case
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81 -scircular1 boolean Sequence is circular
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82 -sformat1 string Input sequence format
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83 -iquery1 string Input query fields or ID list
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84 -ioffset1 integer Input start position offset
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85 -sdbname1 string Database name
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86 -sid1 string Entryname
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87 -ufo1 string UFO features
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88 -fformat1 string Features format
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89 -fopenfile1 string Features file name
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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 gkmertable 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 gkmertable is to an image file.
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118
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119 Data files
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120
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121 None.
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122
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123 Notes
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124
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125 None.
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126
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127 References
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128
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129 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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130 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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131 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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132
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133 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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134 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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135 31, 7.
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136
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137 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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138 Analysis Environment with REST and SOAP Web Service Interfaces,
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139 Nucleic Acids Res., 38, W700-W705.
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140
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141 Warnings
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142
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143 None.
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144
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145 Diagnostic Error Messages
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146
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147 None.
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148
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149 Exit status
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150
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151 It always exits with a status of 0.
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152
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153 Known bugs
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154
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155 None.
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156
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157 See also
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158
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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 goligomersearch Searches oligomers in given sequence
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162 gsignature Calculate oligonucleotide usage (genomic signature)
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163
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164 Author(s)
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165
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166 Hidetoshi Itaya (celery@g-language.org)
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167 Institute for Advanced Biosciences, Keio University
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168 252-0882 Japan
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169
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170 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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171 Institute for Advanced Biosciences, Keio University
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172 252-0882 Japan
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173
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174 History
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175
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176 2012 - Written by Hidetoshi Itaya
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177 2013 - Fixed by Hidetoshi Itaya
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178
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179 Target users
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180
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181 This program is intended to be used by everyone and everything, from
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182 naive users to embedded scripts.
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183
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184 Comments
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185
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186 None.
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187
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