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comparison GEMBASSY-1.0.3/doc/html/ggenomemap3.html @ 0:8300eb051bea draft

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: ggenomemap3 </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 ggenomemap3
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 Draws the map of the genome (version 3)
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 ggenomemap3 creates a map of the genome, showing the local nucleotide<br />
45 contents and positions of genes. A is shown in red, T is shown in green, <br />
46 G is shown in yellow, and C is shown in blue.<br />
47 Created image has a resolution of 8192x8192 and is suited for conversion<br />
48 to SVG, which can be performed by specifying the -format option. The formats<br />
49 available are dependent to the "convert" command from ImageMagick.<br />
50 <br />
51 G-language SOAP service is provided by the<br />
52 Institute for Advanced Biosciences, Keio University.<br />
53 The original web service is located at the following URL:<br />
54 <br />
55 http://www.g-language.org/wiki/soap<br />
56 <br />
57 WSDL(RPC/Encoded) file is located at:<br />
58 <br />
59 http://soap.g-language.org/g-language.wsdl<br />
60 <br />
61 Documentation on G-language Genome Analysis Environment methods are<br />
62 provided at the Document Center<br />
63 <br />
64 http://ws.g-language.org/gdoc/<br />
65 <br />
66
67 </p>
68
69 <H2>Usage</H2>
70
71 Here is a sample session with ggenomemap3
72
73 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
74
75 % ggenomemap3 refseqn:NC_000913
76 Draws the map of the genome (version 3)
77 Created ggenomemap3.1.png
78
79 </pre></td></tr></table>
80
81
82
83 <h2>Command line arguments</h2>
84
85 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
86 <tr bgcolor="#FFFFCC">
87 <th align="left">Qualifier</th>
88 <th align="left">Type</th>
89 <th align="left">Description</th>
90 <th align="left">Allowed values</th>
91 <th align="left">Default</th>
92 </tr>
93
94 <tr bgcolor="#FFFFCC">
95 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
96 </tr>
97
98 <tr bgcolor="#FFFFCC">
99 <td>[-sequence]<br>(Parameter 1)</td>
100 <td>seqall</td>
101 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
102 <td>Readable sequence(s)</td>
103 <td><b>Required</b></td>
104 </tr>
105
106 <tr bgcolor="#FFFFCC">
107 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
108 </tr>
109
110 <tr>
111 <td colspan=5>(none)</td>
112 </tr>
113
114 <tr bgcolor="#FFFFCC">
115 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
116 </tr>
117
118 <tr bgcolor="#FFFFCC">
119 <td>-format</td>
120 <td>string</td>
121 <td>Output file format. Dependent on 'convert' command</td>
122 <td>Any string</td>
123 <td>png</td>
124 </tr>
125
126 <tr bgcolor="#FFFFCC">
127 <td>-width</td>
128 <td>integer</td>
129 <td>Image width</td>
130 <td>Any integer value</td>
131 <td>8192</td>
132 </tr>
133
134 <tr bgcolor="#FFFFCC">
135 <td>-height</td>
136 <td>integer</td>
137 <td>Image height</td>
138 <td>Any integer value</td>
139 <td>8192</td>
140 </tr>
141
142 <tr bgcolor="#FFFFCC">
143 <td>-[no]accid</td>
144 <td>boolean</td>
145 <td>Include to use sequence accession ID as query</td>
146 <td>Boolean value Yes/No</td>
147 <td>Yes</td>
148 </tr>
149
150 <tr bgcolor="#FFFFCC">
151 <td>-goutfile</td>
152 <td>string</td>
153 <td>Output file for non interactive displays</td>
154 <td>Any string</td>
155 <td>ggenomemap3</td>
156 </tr>
157
158 </table>
159
160
161 <h2 id="input">Input file format</h2>
162
163 <p>
164 The database definitions for following commands are available at<br />
165 http://soap.g-language.org/kbws/embossrc<br />
166 <br />
167 ggenomemap3 reads one or more nucleotide sequences.<br />
168 <br />
169
170 </p>
171
172 <h2 id="output">Output file format</h2>
173
174 <p>
175 The output from ggenomemap3 is to an image file.<br />
176 </p>
177
178 <h2>Data files</h2>
179
180 <p>
181 None.
182 </p>
183
184 <h2>Notes</h2>
185
186 <p>
187 None.
188 </p>
189
190 <h2>References</h2>
191
192 <pre>
193 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
194 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
195 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
196
197 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
198 large-scale analysis of high-throughput omics data, J. Pest Sci.,
199 31, 7.
200
201 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
202 Analysis Environment with REST and SOAP Web Service Interfaces,
203 Nucleic Acids Res., 38, W700-W705.
204
205 </pre>
206
207 <h2>Warnings</h2>
208
209 <p>
210 None.
211 </p>
212
213 <h2>Diagnostic Error Messages</h2>
214
215 <p>
216 None.
217 </p>
218
219 <h2>Exit status</h2>
220
221 <p>
222 It always exits with a status of 0.
223 </p>
224
225 <h2>Known bugs</h2>
226
227 <p>
228 None.
229 </p>
230
231 <h2>See also</h2>
232
233 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
234 <th>Description</th></tr>
235
236 <tr>
237 <td><a href="gcircularmap.html">gcircular_map</a></td>
238 <td>Draws circular map of the genome</td>
239 </tr><tr>
240 <td><a href="gdnawalk.html">gdnawalk</a></td>
241 <td>Draws DNA Walk map of the genome</td>
242 </tr>
243
244 </table>
245
246 <h2>Author(s)</h2>
247
248 <pre>
249 Hidetoshi Itaya (celery@g-language.org)
250 Institute for Advanced Biosciences, Keio University
251 252-0882 Japan
252
253 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
254 Institute for Advanced Biosciences, Keio University
255 252-0882 Japan</pre>
256
257 <h2>History</h2>
258
259 2012 - Written by Hidetoshi Itaya
260
261 <h2>Target users</h2>
262
263 This program is intended to be used by everyone and everything, from
264 naive users to embedded scrips.
265
266 <h2>Comments</h2>
267
268 None.
269
270 </BODY>
271 </HTML>