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date Fri, 26 Jun 2015 05:21:44 -0400
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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gkmertable </TITLE>
6 </HEAD>
7 <BODY BGCOLOR="#FFFFFF" text="#000000">
8
9
10
11 <table align=center border=0 cellspacing=0 cellpadding=0>
12 <tr><td valign=top>
13 <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>
14 </td>
15 <td align=left valign=middle>
16 <b><font size="+6">
17 gkmertable
18 </font></b>
19 </td></tr>
20 </table>
21 <br>&nbsp;
22 <p>
23
24
25 <!--END OF HEADER-->
26
27
28
29
30
31
32 <H2> Function </H2>
33 Create an image showing all k-mer abundance within a sequence
34 <!--
35 DON'T WRITE ANYTHING HERE.
36 IT IS DONE FOR YOU.
37 -->
38
39
40
41
42 <H2>Description</H2>
43 <p>
44 gkmertable creates an image showing the abundance of all k-mers<br />
45 (oligonucleotides of length k) in a given sequence. For example, for<br />
46 tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each<br />
47 representing an oligomer. Oligomer name and abundance is written within<br />
48 these boxes, and abundance is also visualized with the box color, from<br />
49 white (none) to black (highly frequent).<br />
50 This k-mer table is alternatively known as the FCGR (frequency matrices<br />
51 extracted from Chaos Game Representation).<br />
52 Position of the oligomers can be recursively located as follows:<br />
53 For each letter in an oligomer, a box is subdivided into four quadrants, <br />
54 where A is upper left, T is lower right, G is upper right, and C is lower<br />
55 left.<br />
56 Therefore, oligomer ATGC is in the <br />
57 A = upper left quadrant<br />
58 T = lower right within the above quadrant<br />
59 G = upper right within the above quadrant<br />
60 C = lower left within the above quadrant<br />
61 More detailed documentation is available at <br />
62 http://www.g-language.org/wiki/cgr<br />
63 <br />
64 G-language SOAP service is provided by the<br />
65 Institute for Advanced Biosciences, Keio University.<br />
66 The original web service is located at the following URL:<br />
67 <br />
68 http://www.g-language.org/wiki/soap<br />
69 <br />
70 WSDL(RPC/Encoded) file is located at:<br />
71 <br />
72 http://soap.g-language.org/g-language.wsdl<br />
73 <br />
74 Documentation on G-language Genome Analysis Environment methods are<br />
75 provided at the Document Center<br />
76 <br />
77 http://ws.g-language.org/gdoc/<br />
78 <br />
79
80 </p>
81
82 <H2>Usage</H2>
83
84 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
85
86 Here is a sample session with gkmertable
87
88 % gkmertable refseqn:NC_000913
89 Create an image showing all k-mer abundance within a sequence
90 Created gkmertable.1.png
91
92 Go to the input files for this example
93 Go to the output files for this example
94
95
96
97 </pre></td></tr></table>
98
99
100
101 <h2>Command line arguments</h2>
102
103 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
104 <tr bgcolor="#FFFFCC">
105 <th align="left">Qualifier</th>
106 <th align="left">Type</th>
107 <th align="left">Description</th>
108 <th align="left">Allowed values</th>
109 <th align="left">Default</th>
110 </tr>
111
112 <tr bgcolor="#FFFFCC">
113 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
114 </tr>
115
116 <tr bgcolor="#FFFFCC">
117 <td>[-sequence]<br>(Parameter 1)</td>
118 <td>seqall</td>
119 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
120 <td>Readable sequence(s)</td>
121 <td><b>Required</b></td>
122 </tr>
123
124 <tr bgcolor="#FFFFCC">
125 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
126 </tr>
127
128 <tr>
129 <td colspan=5>(none)</td>
130 </tr>
131
132 <tr bgcolor="#FFFFCC">
133 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
134 </tr>
135
136 <tr bgcolor="#FFFFCC">
137 <td>-format</td>
138 <td>string</td>
139 <td>Output file format. Dependent on 'convert' command</td>
140 <td>Any string</td>
141 <td>png</td>
142 </tr>
143
144 <tr bgcolor="#FFFFCC">
145 <td>-k</td>
146 <td>integer</td>
147 <td>Length of oligomer</td>
148 <td>Any integer value</td>
149 <td>6</td>
150 </tr>
151
152 <tr bgcolor="#FFFFCC">
153 <td>-goutfile</td>
154 <td>string</td>
155 <td>Output file for non interactive displays</td>
156 <td>Any string</td>
157 <td>gkmertable</td>
158 </tr>
159
160 </table>
161
162
163 <h2 id="input">Input file format</h2>
164
165 <p>
166 The database definitions for following commands are available at<br />
167 http://soap.g-language.org/kbws/embossrc<br />
168 <br />
169 gkmertable reads one or more nucleotide sequences.<br />
170 <br />
171
172 </p>
173
174 <h2 id="output">Output file format</h2>
175
176 <p>
177 The output from gkmertable is to an image file.<br />
178 </p>
179
180 <h2>Data files</h2>
181
182 <p>
183 None.
184 </p>
185
186 <h2>Notes</h2>
187
188 <p>
189 None.
190 </p>
191
192 <h2>References</h2>
193
194 <pre>
195 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
196 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
197 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
198
199 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
200 large-scale analysis of high-throughput omics data, J. Pest Sci.,
201 31, 7.
202
203 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
204 Analysis Environment with REST and SOAP Web Service Interfaces,
205 Nucleic Acids Res., 38, W700-W705.
206
207 </pre>
208
209 <h2>Warnings</h2>
210
211 <p>
212 None.
213 </p>
214
215 <h2>Diagnostic Error Messages</h2>
216
217 <p>
218 None.
219 </p>
220
221 <h2>Exit status</h2>
222
223 <p>
224 It always exits with a status of 0.
225 </p>
226
227 <h2>Known bugs</h2>
228
229 <p>
230 None.
231 </p>
232
233 <h2>See also</h2>
234
235 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
236 <th>Description</th></tr>
237
238 <tr>
239 <td><a href="gnucleotideperiodicity.html">gnucleotideperiodicity</a></td>
240 <td>Checks the periodicity of certain oligonucleotides</td>
241 </tr><tr>
242 <td><a href="goligomercounter.html">goligomercounter</a></td>
243 <td>Counts the number of given oligomers in a sequence</td>
244 </tr><tr>
245 <td><a href="goligomersearch.html">goligomersearch</a></td>
246 <td>Searches oligomers in given sequence</td>
247 </tr><tr>
248 <td><a href="gsignature.html">gsignature</a></td>
249 <td>Calculate oligonucleotide usage (genomic signature)</td>
250 </tr>
251
252 </table>
253
254 <h2>Author(s)</h2>
255
256 <pre>
257 Hidetoshi Itaya (celery@g-language.org)
258 Institute for Advanced Biosciences, Keio University
259 252-0882 Japan
260
261 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
262 Institute for Advanced Biosciences, Keio University
263 252-0882 Japan</pre>
264
265 <h2>History</h2>
266
267 2012 - Written by Hidetoshi Itaya
268
269 <h2>Target users</h2>
270
271 This program is intended to be used by everyone and everything, from
272 naive users to embedded scrips.
273
274 <h2>Comments</h2>
275
276 None.
277
278 </BODY>
279 </HTML>