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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gdnawalk </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 gdnawalk
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 DNA Walk 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 draws the DNA Walk map of the given genome. DNA Walk is drawn by<br />
45 moving a single pixel per nucleotide, in the direction specified for each<br />
46 base. Here A is moved upward, T downward, G to the right, and C to the<br />
47 left. Position zero (first letter of the genome) is indicated by the<br />
48 crossing of thin axes.<br />
49 <br />
50 G-language SOAP service is provided by the<br />
51 Institute for Advanced Biosciences, Keio University.<br />
52 The original web service is located at the following URL:<br />
53 <br />
54 http://www.g-language.org/wiki/soap<br />
55 <br />
56 WSDL(RPC/Encoded) file is located at:<br />
57 <br />
58 http://soap.g-language.org/g-language.wsdl<br />
59 <br />
60 Documentation on G-language Genome Analysis Environment methods are<br />
61 provided at the Document Center<br />
62 <br />
63 http://ws.g-language.org/gdoc/<br />
64 <br />
65
66 </p>
67
68 <H2>Usage</H2>
69
70 Here is a sample session with gdnawalk
71
72 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
73
74 % gdnawalk refseqn:NC_000913
75 Draws DNA Walk map of the genome
76 Created gdnawalk.1.png
77
78 </pre></td></tr></table>
79
80 Go to the <a href="#input">input files</a> for this example<br>
81 Go to the <a href="#output">output files</a> for this example<br><br>
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>-goutfile</td>
128 <td>string</td>
129 <td>Output file for non interactive displays</td>
130 <td>Any string</td>
131 <td>gdnawalk</td>
132 </tr>
133
134 </table>
135
136
137 <h2 id="input">Input file format</h2>
138
139 <p>
140 The database definitions for following commands are available at<br />
141 http://soap.g-language.org/kbws/embossrc<br />
142 <br />
143 gdnawalk reads one or more nucleotide sequences.<br />
144 <br />
145
146 </p>
147
148 <h2 id="output">Output file format</h2>
149
150 <p>
151 The output from gdnawalk is to an image file.<br />
152 </p>
153
154 <h2>Data files</h2>
155
156 <p>
157 None.
158 </p>
159
160 <h2>Notes</h2>
161
162 <p>
163 None.
164 </p>
165
166 <h2>References</h2>
167
168 <pre>
169 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
170 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
171 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
172
173 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
174 large-scale analysis of high-throughput omics data, J. Pest Sci.,
175 31, 7.
176
177 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
178 Analysis Environment with REST and SOAP Web Service Interfaces,
179 Nucleic Acids Res., 38, W700-W705.
180
181 </pre>
182
183 <h2>Warnings</h2>
184
185 <p>
186 None.
187 </p>
188
189 <h2>Diagnostic Error Messages</h2>
190
191 <p>
192 None.
193 </p>
194
195 <h2>Exit status</h2>
196
197 <p>
198 It always exits with a status of 0.
199 </p>
200
201 <h2>Known bugs</h2>
202
203 <p>
204 None.
205 </p>
206
207 <h2>See also</h2>
208
209 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
210 <th>Description</th></tr>
211
212 <tr>
213 <td><a href="gcircularmap.html">gcircularmap</a></td>
214 <td>Draws circular map of the genome</td>
215 </tr><tr>
216 <td><a href="ggenomemap3.html">ggenomemap3</a></td>
217 <td>Draws the map of the genome (version 3)</td>
218 </tr>
219
220 </table>
221
222 <h2>Author(s)</h2>
223
224 <pre>
225 Hidetoshi Itaya (celery@g-language.org)
226 Institute for Advanced Biosciences, Keio University
227 252-0882 Japan
228
229 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
230 Institute for Advanced Biosciences, Keio University
231 252-0882 Japan</pre>
232
233 <h2>History</h2>
234
235 2012 - Written by Hidetoshi Itaya
236
237 <h2>Target users</h2>
238
239 This program is intended to be used by everyone and everything, from
240 naive users to embedded scrips.
241
242 <h2>Comments</h2>
243
244 None.
245