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date Fri, 26 Jun 2015 05:21:44 -0400
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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gfindoriter </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 gfindoriter
18 </font></b>
19 </td></tr>
20 </table>
21 <br>&nbsp;
22 <p>
23
24
25 <!--END OF HEADER-->
26
27
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29
30
31
32 <H2> Function </H2>
33 Predict the replication origin and terminus in bacterial genomes
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 gfindoriter predicts the replicational origin and terminus in circular<br />
45 bacterial genomes, by taking the vertices of cumulative skew graphs (GC,<br />
46 d keto, or purine). See Frank and Lobry (2000) for the basic idea behind<br />
47 this algorithm (but also note that this algorithm is different from that<br />
48 of Oriloc, which uses GC3 of genes). <br />
49 Terminus of replication can be more accurate by using noise-reduction <br />
50 filtering using Fourier spectrum of the GC skew. This low-pass filtering<br />
51 can be applied using -filter option. See Arakawa et al. (2007) for details.<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 gfindoriter
74
75 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
76
77 % gfindoriter refseqn:NC_000913
78 Predict the replication origin and terminus in bacterial genomes
79 Output file [nc_000913.gfindoriter]:
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 <td>[-outfile]<br>(Parameter 2)</td>
111 <td>outfile</td>
112 <td>Output file name</td>
113 <td>Output file</td>
114 <td><i>&lt;*&gt;</i>.gfindoriter</td>
115 </tr>
116
117 <tr bgcolor="#FFFFCC">
118 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
119 </tr>
120
121 <tr>
122 <td colspan=5>(none)</td>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
127 </tr>
128
129 <tr bgcolor="#FFFFCC">
130 <td>-window</td>
131 <td>integer</td>
132 <td>Number of windows to use for Fat Fourier Transform. Only active when -lowpass option is specified. Value must be the power of two</td>
133 <td>Any integer value</td>
134 <td>4096</td>
135 </tr>
136
137 <tr bgcolor="#FFFFCC">
138 <td>-purine</td>
139 <td>boolean</td>
140 <td>Use purine skew for calculation</td>
141 <td>Boolean value Yes/No</td>
142 <td>No</td>
143 </tr>
144
145 <tr bgcolor="#FFFFCC">
146 <td>-keto</td>
147 <td>boolean</td>
148 <td>Use keto skew for calculation</td>
149 <td>Boolean value Yes/No</td>
150 <td>No</td>
151 </tr>
152
153 <tr bgcolor="#FFFFCC">
154 <td>-lowpass</td>
155 <td>integer</td>
156 <td>Lowpass filter strength in percent. Typically 95 or 99 works best</td>
157 <td>Any integer value</td>
158 <td>0</td>
159 </tr>
160
161 <tr bgcolor="#FFFFCC">
162 <td>-[no]accid</td>
163 <td>boolean</td>
164 <td>Include to use sequence accession ID as query</td>
165 <td>Boolean value Yes/No</td>
166 <td>Yes</td>
167 </tr>
168
169 </table>
170
171
172 <h2 id="input">Input file format</h2>
173
174 <p>
175 The database definitions for following commands are available at<br />
176 http://soap.g-language.org/kbws/embossrc<br />
177 <br />
178 gfindoriter reads one or more nucleotide sequences.<br />
179 <br />
180
181 </p>
182
183 <h2 id="output">Output file format</h2>
184
185 <p>
186 The output from gfindoriter is to a plain text file.<br />
187 <br />
188 File: nc_000913.gfindoriter<br />
189 <br />?<table width="90%"><tr><td bgcolor="#CCFFCC">
190 Sequence: NC_000913 Origin: 3922946 Terminus: 1550274<br />
191 </td></tr></table>
192
193 </p>
194
195 <h2>Data files</h2>
196
197 <p>
198 None.
199 </p>
200
201 <h2>Notes</h2>
202
203 <p>
204 None.
205 </p>
206
207 <h2>References</h2>
208
209 <pre>
210 Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in
211 unannotated bacterial chromosomes, Bioinformatics, 16:566-567.
212
213 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
214 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
215 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
216
217 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
218 large-scale analysis of high-throughput omics data, J. Pest Sci.,
219 31, 7.
220
221 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
222 Analysis Environment with REST and SOAP Web Service Interfaces,
223 Nucleic Acids Res., 38, W700-W705.
224
225 </pre>
226
227 <h2>Warnings</h2>
228
229 <p>
230 None.
231 </p>
232
233 <h2>Diagnostic Error Messages</h2>
234
235 <p>
236 None.
237 </p>
238
239 <h2>Exit status</h2>
240
241 <p>
242 It always exits with a status of 0.
243 </p>
244
245 <h2>Known bugs</h2>
246
247 <p>
248 None.
249 </p>
250
251 <h2>See also</h2>
252
253 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
254 <th>Description</th></tr>
255
256 <tr>
257 <td><a href="greporiter.html">greporiter</a></td>
258 <td>Gets the positions of replication origin and terminus</td>
259 </tr>
260
261 </table>
262
263 <h2>Author(s)</h2>
264
265 <pre>
266 Hidetoshi Itaya (celery@g-language.org)
267 Institute for Advanced Biosciences, Keio University
268 252-0882 Japan
269
270 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
271 Institute for Advanced Biosciences, Keio University
272 252-0882 Japan</pre>
273
274 <h2>History</h2>
275
276 2012 - Written by Hidetoshi Itaya
277
278 <h2>Target users</h2>
279
280 This program is intended to be used by everyone and everything, from
281 naive users to embedded scripts.
282
283 <h2>Comments</h2>
284
285 None.
286
287 </BODY>
288 </HTML>