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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gnucleotideperiodicity </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 gnucleotideperiodicity
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 Checks the periodicity of certain oligonucleotides
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 gnucleotideperiodicity checks the periodicity of certain nucleotide<br>
45 (best known with AA dinucleotide). Bacteria and archaebacteria are<br>
46 known to show periodicity of ApA dinucleotides at about 11bp and 10bp.<br>
47 Lower eukaryotes also show periodicity but higher eukaryotes do not.<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 gnucleotideperiodicity
70
71 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
72
73 % gnucleotideperiodicity refseqn:NC_000913
74 Checks the periodicity of certain oligonucleotides
75 Program compseq output file (optional) [nc_000913.gnucleotideperiodicity]:
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 Example 2
83
84 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>?
85 % gnucleotideperiodicity refseqn:NC_000913 -plot -graph png
86 Checks the periodicity of certain oligonucleotides
87 Created gnucleotideperiodicity.1.png
88
89 </pre></td></tr></table>
90
91 Go to the <a href="#input">input files</a> for this example<br>
92 Go to the <a href="#output">output files</a> for this example<br><br>
93
94 <h2>Command line arguments</h2>
95
96 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
97 <tr bgcolor="#FFFFCC">
98 <th align="left">Qualifier</th>
99 <th align="left">Type</th>
100 <th align="left">Description</th>
101 <th align="left">Allowed values</th>
102 <th align="left">Default</th>
103 </tr>
104
105 <tr bgcolor="#FFFFCC">
106 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
107 </tr>
108
109 <tr bgcolor="#FFFFCC">
110 <td>[-sequence]<br>(Parameter 1)</td>
111 <td>seqall</td>
112 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
113 <td>Readable sequence(s)</td>
114 <td><b>Required</b></td>
115 </tr>
116
117 <tr bgcolor="#FFFFCC">
118 <td>-graph</td>
119 <td>xygraph</td>
120 <td>Graph type</td>
121 <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td>
122 <td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <td>-outfile</td>
127 <td>outfile</td>
128 <td>Program compseq output file (optional)</td>
129 <td>Output file</td>
130 <td><i>&lt;*&gt;</i>.gnucleotideperiodicity</td>
131 </tr>
132
133 <tr bgcolor="#FFFFCC">
134 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
135 </tr>
136
137 <tr>
138 <td colspan=5>(none)</td>
139 </tr>
140
141 <tr bgcolor="#FFFFCC">
142 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
143 </tr>
144
145 <tr bgcolor="#FFFFCC">
146 <td>-format</td>
147 <td>string</td>
148 <td>Output file format. Dependent on 'convert' command</td>
149 <td>Any string</td>
150 <td>png</td>
151 </tr>
152
153 <tr bgcolor="#FFFFCC">
154 <td>-window</td>
155 <td>integer</td>
156 <td>Window size to seek periodicity</td>
157 <td>Any integer value</td>
158 <td>50</td>
159 </tr>
160
161 <tr bgcolor="#FFFFCC">
162 <td>-nucleotide</td>
163 <td>string</td>
164 <td>Nucleotide to search</td>
165 <td>Any string</td>
166 <td>aa</td>
167 </tr>
168
169 <tr bgcolor="#FFFFCC">
170 <td>-[no]accid</td>
171 <td>boolean</td>
172 <td>Include to use sequence accession ID as query</td>
173 <td>Boolean value Yes/No</td>
174 <td>Yes</td>
175 </tr>
176
177 <tr bgcolor="#FFFFCC">
178 <td>-plot</td>
179 <td>toggle</td>
180 <td>Include to plot result</td>
181 <td>Toggle value Yes/No</td>
182 <td>No</td>
183 </tr>
184
185 </table>
186
187
188 <h2 id="input">Input file format</h2>
189
190 <p>
191 The database definitions for following commands are available at<br />
192 http://soap.g-language.org/kbws/embossrc<br />
193 <br />
194 gnucleotideperiodicity reads one or more nucleotide sequences.<br />
195 <br />
196
197 </p>
198
199 <h2 id="output">Output file format</h2>
200
201 <p>
202 The output from gnucleotideperiodicity is to a plain text file or the EMBOSS graphics device.<br />
203 <br />
204 File: nc_000913.gnucleotideperiodicity<br />
205 <br /></td></tr></table>
206 <table width="90%"><tr><td bgcolor="#CCFFCC">
207 Sequence: NC_000913<br />
208 window,value<br />
209 0,35134<br />
210 1,30121<br />
211 2,25409<br />
212 3,23508<br />
213 4,25830<br />
214 5,25136<br />
215 6,25658<br />
216 7,28279<br />
217 <br />
218 <font color=red>[Part of this file has been deleted for brevity]</font><br />
219 <br />
220 40,28042<br />
221 41,25892<br />
222 42,25968<br />
223 43,28240<br />
224 44,25841<br />
225 45,25591<br />
226 46,27788<br />
227 47,25832<br />
228 48,25427<br />
229 49,0<br />
230 </td></tr></table>
231
232 </p>
233
234 <h2>Data files</h2>
235
236 <p>
237 None.
238 </p>
239
240 <h2>Notes</h2>
241
242 <p>
243 None.
244 </p>
245
246 <h2>References</h2>
247
248 <pre>
249 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
250 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
251 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
252
253 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
254 large-scale analysis of high-throughput omics data, J. Pest Sci.,
255 31, 7.
256
257 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
258 Analysis Environment with REST and SOAP Web Service Interfaces,
259 Nucleic Acids Res., 38, W700-W705.
260
261 </pre>
262
263 <h2>Warnings</h2>
264
265 <p>
266 None.
267 </p>
268
269 <h2>Diagnostic Error Messages</h2>
270
271 <p>
272 None.
273 </p>
274
275 <h2>Exit status</h2>
276
277 <p>
278 It always exits with a status of 0.
279 </p>
280
281 <h2>Known bugs</h2>
282
283 <p>
284 None.
285 </p>
286
287 <h2>See also</h2>
288
289 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
290 <th>Description</th></tr>
291
292 <tr>
293 <td><a href="gkmertable.html">gkmertable</a></td>
294 <td>Create an image showing all k-mer abundance within a sequence</td>
295 </tr><tr>
296 <td><a href="goligomercounter.html">goligomercounter</a></td>
297 <td>Counts the number of given oligomers in a sequence</td>
298 </tr><tr>
299 <td><a href="goligomersearch.html">goligomersearch</a></td>
300 <td>Searches oligomers in given sequence</td>
301 </tr><tr>
302 <td><a href="gsignature.html">gsignature</a></td>
303 <td>Calculate oligonucleotide usage (genomic signature)</td>
304 </tr>
305
306 </table>
307
308 <h2>Author(s)</h2>
309
310 <pre>
311 Hidetoshi Itaya (celery@g-language.org)
312 Institute for Advanced Biosciences, Keio University
313 252-0882 Japan
314
315 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
316 Institute for Advanced Biosciences, Keio University
317 252-0882 Japan</pre>
318
319 <h2>History</h2>
320
321 2012 - Written by Hidetoshi Itaya
322
323 <h2>Target users</h2>
324
325 This program is intended to be used by everyone and everything, from
326 naive users to embedded scrips.
327
328 <h2>Comments</h2>
329
330 None.
331
332 </BODY>
333 </HTML>