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comparison GEMBASSY-1.0.3/doc/html/gseq2png.html @ 0:8300eb051bea draft

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gseq2png </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 gseq2png
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 Converts a sequence to PNG image
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 gseq2png converts a sequence to a png image, by representing nucleotide<br />
45 sequences with representative pixels. A is shown in red, T is shown in<br />
46 green, G is shown in yellow, and C is shown in blue.<br />
47 <br />
48 G-language SOAP service is provided by the<br />
49 Institute for Advanced Biosciences, Keio University.<br />
50 The original web service is located at the following URL:<br />
51 <br />
52 http://www.g-language.org/wiki/soap<br />
53 <br />
54 WSDL(RPC/Encoded) file is located at:<br />
55 <br />
56 http://soap.g-language.org/g-language.wsdl<br />
57 <br />
58 Documentation on G-language Genome Analysis Environment methods are<br />
59 provided at the Document Center<br />
60 <br />
61 http://ws.g-language.org/gdoc/<br />
62 <br />
63
64 </p>
65
66 <H2>Usage</H2>
67
68 Here is a sample session with gseq2png
69
70 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
71
72 % gseq2png refseqn:NC_000913
73 Converts a sequence to PNG image
74 Created gseq2png.1.png
75
76 </pre></td></tr></table>
77
78 Go to the <a href="#input">input files</a> for this example<br>
79 Go to the <a href="#output">output files</a> for this example<br><br>
80
81 <h2>Command line arguments</h2>
82
83 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
84 <tr bgcolor="#FFFFCC">
85 <th align="left">Qualifier</th>
86 <th align="left">Type</th>
87 <th align="left">Description</th>
88 <th align="left">Allowed values</th>
89 <th align="left">Default</th>
90 </tr>
91
92 <tr bgcolor="#FFFFCC">
93 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
94 </tr>
95
96 <tr bgcolor="#FFFFCC">
97 <td>[-sequence]<br>(Parameter 1)</td>
98 <td>seqall</td>
99 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
100 <td>Readable sequence(s)</td>
101 <td><b>Required</b></td>
102 </tr>
103
104 <tr bgcolor="#FFFFCC">
105 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
106 </tr>
107
108 <tr>
109 <td colspan=5>(none)</td>
110 </tr>
111
112 <tr bgcolor="#FFFFCC">
113 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
114 </tr>
115
116 <tr bgcolor="#FFFFCC">
117 <td>-format</td>
118 <td>string</td>
119 <td>Output file format. Dependent on 'convert' command</td>
120 <td>Any string</td>
121 <td>png</td>
122 </tr>
123
124 <tr bgcolor="#FFFFCC">
125 <td>-width</td>
126 <td>integer</td>
127 <td>Width of the image</td>
128 <td>Any integer value</td>
129 <td>640</td>
130 </tr>
131
132 <tr bgcolor="#FFFFCC">
133 <td>-window</td>
134 <td>integer</td>
135 <td>Window size of a sequence to represent each pixel</td>
136 <td>Any integer value</td>
137 <td>20</td>
138 </tr>
139
140 <tr bgcolor="#FFFFCC">
141 <td>-goutfile</td>
142 <td>string</td>
143 <td>Output file for non interactive displays</td>
144 <td>Any string</td>
145 <td>gcgr</td>
146 </tr>
147
148 </table>
149
150
151 <h2 id="input">Input file format</h2>
152
153 <p>
154 The database definitions for following commands are available at<br />
155 http://soap.g-language.org/kbws/embossrc<br />
156 <br />
157 gseq2png reads one or more nucleotide sequences.<br />
158 <br />
159
160 </p>
161
162 <h2 id="output">Output file format</h2>
163
164 <p>
165 The output from gseq2png is to an image file.<br />
166 </p>
167
168 <h2>Data files</h2>
169
170 <p>
171 None.
172 </p>
173
174 <h2>Notes</h2>
175
176 <p>
177 None.
178 </p>
179
180 <h2>References</h2>
181
182 <pre>
183 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
184 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
185 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
186
187 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
188 large-scale analysis of high-throughput omics data, J. Pest Sci.,
189 31, 7.
190
191 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
192 Analysis Environment with REST and SOAP Web Service Interfaces,
193 Nucleic Acids Res., 38, W700-W705.
194
195 </pre>
196
197 <h2>Warnings</h2>
198
199 <p>
200 None.
201 </p>
202
203 <h2>Diagnostic Error Messages</h2>
204
205 <p>
206 None.
207 </p>
208
209 <h2>Exit status</h2>
210
211 <p>
212 It always exits with a status of 0.
213 </p>
214
215 <h2>Known bugs</h2>
216
217 <p>
218 None.
219 </p>
220
221 <h2>See also</h2>
222
223 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
224 <th>Description</th></tr>
225
226 <tr>
227 <td><a href="gcgr.html">gcgr</a></td>
228 <td>Create a Chaos Game Representation of a given sequence</td>
229 </tr>
230
231 </table>
232
233 <h2>Author(s)</h2>
234
235 <pre>
236 Hidetoshi Itaya (celery@g-language.org)
237 Institute for Advanced Biosciences, Keio University
238 252-0882 Japan
239
240 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
241 Institute for Advanced Biosciences, Keio University
242 252-0882 Japan</pre>
243
244 <h2>History</h2>
245
246 2012 - Written by Hidetoshi Itaya
247
248 <h2>Target users</h2>
249
250 This program is intended to be used by everyone and everything, from
251 naive users to embedded scrips.
252
253 <h2>Comments</h2>
254
255 None.
256