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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gcircularmap </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 gcircularmap
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 circular map of the genome
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 gdnawalk creates a circular map of the genome using SVG, suitable for<br />
45 plasmids and circular bacterial chromosomes.<br />
46 From the outer ring inwards, genes on direct strand (pink), <br />
47 genes on complementary strand (yellow), tRNAs (green arrows), <br />
48 rRNAs (pink or orange stripes depending on the strand), <br />
49 GC content (brown lines), GC skew (yellow lines). Replication <br />
50 origin and terminus predicted from the GC skew shift points <br />
51 are also labeled. <br />
52 <br />
53 G-language SOAP service is provided by the<br />
54 Institute for Advanced Biosciences, Keio University.<br />
55 The original web service is located at the following URL:<br />
56 <br />
57 http://www.g-language.org/wiki/soap<br />
58 <br />
59 WSDL(RPC/Encoded) file is located at:<br />
60 <br />
61 http://soap.g-language.org/g-language.wsdl<br />
62 <br />
63 Documentation on G-language Genome Analysis Environment methods are<br />
64 provided at the Document Center<br />
65 <br />
66 http://ws.g-language.org/gdoc/<br />
67 <br />
68
69 </p>
70
71 <H2>Usage</H2>
72
73 Here is a sample session with gcircularmap
74
75 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
76
77 % gcircularmap refseqn:NC_000913
78 Draws circular map of the genome
79 Created gcircularmap.1.svg
80
81 </pre></td></tr></table>
82
83 Go to the <a href="#input">input files</a> for this example<br>
84 Go to the <a href="#output">output files</a> for this example<br><br>
85
86 <h2>Command line arguments</h2>
87
88 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
89 <tr bgcolor="#FFFFCC">
90 <th align="left">Qualifier</th>
91 <th align="left">Type</th>
92 <th align="left">Description</th>
93 <th align="left">Allowed values</th>
94 <th align="left">Default</th>
95 </tr>
96
97 <tr bgcolor="#FFFFCC">
98 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
99 </tr>
100
101 <tr bgcolor="#FFFFCC">
102 <td>[-sequence]<br>(Parameter 1)</td>
103 <td>seqall</td>
104 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
105 <td>Readable sequence(s)</td>
106 <td><b>Required</b></td>
107 </tr>
108
109 <tr bgcolor="#FFFFCC">
110 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
111 </tr>
112
113 <tr>
114 <td colspan=5>(none)</td>
115 </tr>
116
117 <tr bgcolor="#FFFFCC">
118 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
119 </tr>
120
121 <tr bgcolor="#FFFFCC">
122 <td>-format</td>
123 <td>string</td>
124 <td>Output file format. Dependent on 'convert' command</td>
125 <td>Any string</td>
126 <td>svg</td>
127 </tr>
128
129 <tr bgcolor="#FFFFCC">
130 <td>-[no]accid</td>
131 <td>boolean</td>
132 <td>Include to use sequence accession ID as query</td>
133 <td>Boolean value Yes/No</td>
134 <td>Yes</td>
135 </tr>
136
137 <tr bgcolor="#FFFFCC">
138 <td>-goutfile</td>
139 <td>string</td>
140 <td>Output file for non interactive displays</td>
141 <td>Any string</td>
142 <td>gcircularmap</td>
143 </tr>
144
145 </table>
146
147
148 <h2 id="input">Input file format</h2>
149
150 <p>
151 The database definitions for following commands are available at<br />
152 http://soap.g-language.org/kbws/embossrc<br />
153 <br />
154 gcircularmap reads one or more nucleotide sequences.<br />
155 <br />
156
157 </p>
158
159 <h2 id="output">Output file format</h2>
160
161 <p>
162 The output from gcircularmap is to an image file.
163 </p>
164
165 <h2>Data files</h2>
166
167 <p>
168 None.
169 </p>
170
171 <h2>Notes</h2>
172
173 <p>
174 None.
175 </p>
176
177 <h2>References</h2>
178
179 <pre>
180 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
181 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
182 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
183
184 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
185 large-scale analysis of high-throughput omics data, J. Pest Sci.,
186 31, 7.
187
188 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
189 Analysis Environment with REST and SOAP Web Service Interfaces,
190 Nucleic Acids Res., 38, W700-W705.
191
192 </pre>
193
194 <h2>Warnings</h2>
195
196 <p>
197 None.
198 </p>
199
200 <h2>Diagnostic Error Messages</h2>
201
202 <p>
203 None.
204 </p>
205
206 <h2>Exit status</h2>
207
208 <p>
209 It always exits with a status of 0.
210 </p>
211
212 <h2>Known bugs</h2>
213
214 <p>
215 None.
216 </p>
217
218 <h2>See also</h2>
219
220 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
221 <th>Description</th></tr>
222
223 <tr>
224 <td><a href="gdnawalk.html">gdnawalk</a></td>
225 <td>Draws DNA Walk map of the genome</td>
226 </tr><tr>
227 <td><a href="ggenomemap3.html">ggenomemap3</a></td>
228 <td>Draws the map of the genome (version 3)</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
257 </BODY>
258 </HTML>