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comparison GEMBASSY-1.0.3/doc/html/gcgr.html @ 0:8300eb051bea draft

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author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gcgr </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 gcgr
18 </font></b>
19 </td></tr>
20 </table>
21 <br>&nbsp;
22 <p>
23
24
25 <!--END OF HEADER-->
26
27
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29
30
31
32 <H2> Function </H2>
33 Create a Chaos Game Representation of a given 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 gcgr creates a Chaos Game Representation (CGR) image of a given sequence.
45 CGR is generated by the following procedure:<br />
46 <br />
47 1. Start from position (0,0) or the origin of two dimensional coordinate.<br />
48 Four nucleotides are located at the four corners:<br />
49 A: (-1, 1) upper left<br />
50 T: (1, -1) lower right<br />
51 G: (1, 1) upper right<br />
52 C: (-1, -1) lower left<br />
53 2. For each nucleotide, move and mark the new location which is halfway<br />
54 between the current location and the nucleotide.<br />
55 For example, if the first letter is A, position is moved from (0,0) to<br />
56 midpoint between (-1, 1) and (0,0), which is (-0.5, 0.5).<br />
57 <br />
58 3. Repeat this procedure for all nucleotides.<br />
59 CGR is a generalized scale-independent Markov probability table for the<br />
60 sequence, and oligomer tables can be deduced from CGR image.<br />
61 <br />
62 G-language SOAP service is provided by the<br />
63 Institute for Advanced Biosciences, Keio University.<br />
64 The original web service is located at the following URL:<br />
65 <br />
66 http://www.g-language.org/wiki/soap<br />
67 <br />
68 WSDL(RPC/Encoded) file is located at:<br />
69 <br />
70 http://soap.g-language.org/g-language.wsdl<br />
71 <br />
72 Documentation on G-language Genome Analysis Environment methods are<br />
73 provided at the Document Center<br />
74 <br />
75 http://ws.g-language.org/gdoc/<br />
76 <br />
77
78 </p>
79
80 <H2>Usage</H2>
81
82 Here is a sample session with gcgr
83
84 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
85
86 % gcgr refseqn:NC_000913
87 Create a Chaos Game Representation of a given sequence
88 Created gcgr.1.png
89
90 </pre></td></tr></table>
91
92 Go to the <a href="#input">input files</a> for this example<br>
93 Go to the <a href="#output">output files</a> for this example<br><br>
94
95 <h2>Command line arguments</h2>
96
97 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
98 <tr bgcolor="#FFFFCC">
99 <th align="left">Qualifier</th>
100 <th align="left">Type</th>
101 <th align="left">Description</th>
102 <th align="left">Allowed values</th>
103 <th align="left">Default</th>
104 </tr>
105
106 <tr bgcolor="#FFFFCC">
107 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
108 </tr>
109
110 <tr bgcolor="#FFFFCC">
111 <td>[-sequence]<br>(Parameter 1)</td>
112 <td>seqall</td>
113 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
114 <td>Readable sequence(s)</td>
115 <td><b>Required</b></td>
116 </tr>
117
118 <tr bgcolor="#FFFFCC">
119 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
120 </tr>
121
122 <tr>
123 <td colspan=5>(none)</td>
124 </tr>
125
126 <tr bgcolor="#FFFFCC">
127 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
128 </tr>
129
130 <tr bgcolor="#FFFFCC">
131 <td>-format</td>
132 <td>string</td>
133 <td>Output file format. Dependent on 'convert' command</td>
134 <td>Any string</td>
135 <td>png</td>
136 </tr>
137
138 <tr bgcolor="#FFFFCC">
139 <td>-width</td>
140 <td>integer</td>
141 <td>Width of image</td>
142 <td>Any integer value</td>
143 <td>1024</td>
144 </tr>
145
146 <tr bgcolor="#FFFFCC">
147 <td>-goutfile</td>
148 <td>string</td>
149 <td>Output file for non interactive displays</td>
150 <td>Any string</td>
151 <td>gcgr</td>
152 </tr>
153
154 </table>
155
156
157 <h2 id="input">Input file format</h2>
158
159 <p>
160 The database definitions for following commands are available at<br />
161 http://soap.g-language.org/kbws/embossrc<br />
162 <br />
163 gcgr reads one or more nucleotide sequences.<br />
164 <br />
165
166 </p>
167
168 <h2 id="output">Output file format</h2>
169
170 <p>
171 The output from gcgr is to an image file.
172 </p>
173
174 <h2>Data files</h2>
175
176 <p>
177 None.
178 </p>
179
180 <h2>Notes</h2>
181
182 <p>
183 None.
184 </p>
185
186 <h2>References</h2>
187
188 <pre>
189 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
190 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
191 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
192
193 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
194 large-scale analysis of high-throughput omics data, J. Pest Sci.,
195 31, 7.
196
197 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
198 Analysis Environment with REST and SOAP Web Service Interfaces,
199 Nucleic Acids Res., 38, W700-W705.
200
201 </pre>
202
203 <h2>Warnings</h2>
204
205 <p>
206 None.
207 </p>
208
209 <h2>Diagnostic Error Messages</h2>
210
211 <p>
212 None.
213 </p>
214
215 <h2>Exit status</h2>
216
217 <p>
218 It always exits with a status of 0.
219 </p>
220
221 <h2>Known bugs</h2>
222
223 <p>
224 None.
225 </p>
226
227 <h2>See also</h2>
228
229 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
230 <th>Description</th></tr>
231
232 <tr>
233 <td><a href="gseq2png.html">gseq2png</a></td>
234 <td>Converts a sequence to PNG image</td>
235 </tr>
236
237 </table>
238
239 <h2>Author(s)</h2>
240
241 <pre>
242 Hidetoshi Itaya (celery@g-language.org)
243 Institute for Advanced Biosciences, Keio University
244 252-0882 Japan
245
246 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
247 Institute for Advanced Biosciences, Keio University
248 252-0882 Japan</pre>
249
250 <h2>History</h2>
251
252 2012 - Written by Hidetoshi Itaya
253
254 <h2>Target users</h2>
255
256 This program is intended to be used by everyone and everything, from
257 naive users to embedded scrips.
258
259 <h2>Comments</h2>
260
261 None.
262
263 </BODY>
264 </HTML>