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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gsignature </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 gsignature
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 Calculate oligonucleotide usage (genomic signature)
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 gsignature calculates short oligonuleotide usage (genomic signture),<br />
45 defined as the ratio of observed (O) to expected (E) oligonucleotide<br />
46 frequencies. It is known that the genomic signature stays constant<br />
47 throughout the genome.<br />
48 <br />
49 G-language SOAP service is provided by the<br />
50 Institute for Advanced Biosciences, Keio University.<br />
51 The original web service is located at the following URL:<br />
52 <br />
53 http://www.g-language.org/wiki/soap<br />
54 <br />
55 WSDL(RPC/Encoded) file is located at:<br />
56 <br />
57 http://soap.g-language.org/g-language.wsdl<br />
58 <br />
59 Documentation on G-language Genome Analysis Environment methods are<br />
60 provided at the Document Center<br />
61 <br />
62 http://ws.g-language.org/gdoc/<br />
63 <br />
64
65 </p>
66
67 <H2>Usage</H2>
68
69 Here is a sample session with gsignature
70
71 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
72
73 % gsignature refseqn:NC_000913
74 Calculate oligonucleotide usage (genomic signature)
75 Program compseq output file [nc_000913.gsignature]:
76
77 </pre></td></tr></table>
78
79 Go to the <a href="#input">input files</a> for this example<br>
80 Go to the <a href="#output">output files</a> for this example<br><br>
81
82 <h2>Command line arguments</h2>
83
84 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
85 <tr bgcolor="#FFFFCC">
86 <th align="left">Qualifier</th>
87 <th align="left">Type</th>
88 <th align="left">Description</th>
89 <th align="left">Allowed values</th>
90 <th align="left">Default</th>
91 </tr>
92
93 <tr bgcolor="#FFFFCC">
94 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
95 </tr>
96
97 <tr bgcolor="#FFFFCC">
98 <td>[-sequence]<br>(Parameter 1)</td>
99 <td>seqall</td>
100 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
101 <td>Readable sequence(s)</td>
102 <td><b>Required</b></td>
103 </tr>
104
105 <tr bgcolor="#FFFFCC">
106 <td>[-outfile]<br>(Parameter 2)</td>
107 <td>outfile</td>
108 <td>Program compseq output file</td>
109 <td>Output file</td>
110 <td><i>&lt;*&gt;</i>.gsignature</td>
111 </tr>
112
113 <tr bgcolor="#FFFFCC">
114 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
115 </tr>
116
117 <tr>
118 <td colspan=5>(none)</td>
119 </tr>
120
121 <tr bgcolor="#FFFFCC">
122 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <td>-wordlength</td>
127 <td>integer</td>
128 <td>Word length</td>
129 <td>Any integer value</td>
130 <td>2</td>
131 </tr>
132
133 <tr bgcolor="#FFFFCC">
134 <td>-[no]bothstrand</td>
135 <td>boolean</td>
136 <td>Include to use both strands direct used otherwise</td>
137 <td>Boolean value Yes/No</td>
138 <td>Yes</td>
139 </tr>
140
141 <tr bgcolor="#FFFFCC">
142 <td>-[no]oe</td>
143 <td>boolean</td>
144 <td>Include to use O/E value observed values used otherwise</td>
145 <td>Boolean value Yes/No</td>
146 <td>Yes</td>
147 </tr>
148
149 <tr bgcolor="#FFFFCC">
150 <td>-[no]accid</td>
151 <td>boolean</td>
152 <td>Include to use sequence accession ID as query</td>
153 <td>Boolean value Yes/No</td>
154 <td>Yes</td>
155 </tr>
156
157 </table>
158
159
160 <h2>Input file format</h2>
161
162 <p>
163 The database definitions for following commands are available at<br />
164 http://soap.g-language.org/kbws/embossrc<br />
165 <br />
166 gsignature reads one or more nucleotide sequences.<br />
167 <br />
168
169 </p>
170
171 <h2>Output file format</h2>
172
173 <p>
174 The output from gsignature is to a plain text file.<br />
175 <br />
176 File: nc_000913.gsignature<br />
177 <br />
178 <table width="90%"><tr><td bgcolor="#CCFFCC">
179 Sequence: NC_000913<br />
180 aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,memo<br />
181 1.206,0.884,0.817,1.103,1.117,0.905,1.159,0.817,0.922,1.283,0.905,0.884,0.755,0.922,1.117,1.206,<br />
182 </td></tr></table>
183
184 </p>
185
186 <h2>Data files</h2>
187
188 <p>
189 None.
190 </p>
191
192 <h2>Notes</h2>
193
194 <p>
195 None.
196 </p>
197
198 <h2>References</h2>
199
200 <pre>
201 Campbell A et al. (1999) Genome signature comparisons among prokaryote,
202 plasmid, and mitochondrial DNA, Proc Natl Acad Sci U S A. 96(16):9184-9.
203
204 Karlin S. (2001) Detecting anomalous gene clusters and pathogenicity islands
205 in diverse bacterial genomes, Trends Microbiol. 9(7):335-43.
206 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
207 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
208 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
209
210 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
211 large-scale analysis of high-throughput omics data, J. Pest Sci.,
212 31, 7.
213
214 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
215 Analysis Environment with REST and SOAP Web Service Interfaces,
216 Nucleic Acids Res., 38, W700-W705.
217
218 </pre>
219
220 <h2>Warnings</h2>
221
222 <p>
223 None.
224 </p>
225
226 <h2>Diagnostic Error Messages</h2>
227
228 <p>
229 None.
230 </p>
231
232 <h2>Exit status</h2>
233
234 <p>
235 It always exits with a status of 0.
236 </p>
237
238 <h2>Known bugs</h2>
239
240 <p>
241 None.
242 </p>
243
244 <h2>See also</h2>
245
246 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
247 <th>Description</th></tr>
248
249 <tr>
250 <td><a href="gkmertable.html">gkmertable</a></td>
251 <td>Create an image showing all k-mer abundance within a sequence</td>
252 </tr><tr>
253 <td><a href="gnucleotideperiodicity.html">gnucleotideperiodicity</a></td>
254 <td>Checks the periodicity of certain oligonucleotides</td>
255 </tr><tr>
256 <td><a href="goligomercounter.html">goligomercounter</a></td>
257 <td>Counts the number of given oligomers in a sequence</td>
258 </tr><tr>
259 <td><a href="goligomersearch.html">goligomersearch</a></td>
260 <td>Searches oligomers in given sequence</td>
261 </tr>
262
263 </table>
264
265 <h2>Author(s)</h2>
266
267 <pre>
268 Hidetoshi Itaya (celery@g-language.org)
269 Institute for Advanced Biosciences, Keio University
270 252-0882 Japan
271
272 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
273 Institute for Advanced Biosciences, Keio University
274 252-0882 Japan</pre>
275
276 <h2>History</h2>
277
278 2012 - Written by Hidetoshi Itaya
279
280 <h2>Target users</h2>
281
282 This program is intended to be used by everyone and everything, from
283 naive users to embedded scrips.
284
285 <h2>Comments</h2>
286
287 None.
288