Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/doc/html/gdeltagcskew.html @ 0:8300eb051bea draft
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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1 <!--START OF HEADER - DON'T ALTER --> | |
2 | |
3 <HTML> | |
4 <HEAD> | |
5 <TITLE> EMBOSS: gdeltagcskew </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 gdeltagcskew | |
18 </font></b> | |
19 </td></tr> | |
20 </table> | |
21 <br> | |
22 <p> | |
23 | |
24 | |
25 <!--END OF HEADER--> | |
26 | |
27 | |
28 | |
29 | |
30 | |
31 | |
32 <H2> Function </H2> | |
33 Calculate strand bias of bacterial genome using delta GC skew index | |
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 gdeltagcskew calculates strand bias of bacterial genome using delta GC skew<br /> | |
45 index, first proposed by Rocha et al. (2001), and further extended in 2006.<br /> | |
46 Basic idea of delta GC skew index is to calculate the difference of GC skew<br /> | |
47 in coding regions residing in leading and lagging strands. Rocha et al.<br /> | |
48 (2001) calculates delta GC skew index using the third codon position of<br /> | |
49 genes, and Rocha et al. (2006) modified to only use >fourfold degenerate<br /> | |
50 codons.<br /> | |
51 <br /> | |
52 G-language SOAP service is provided by the<br /> | |
53 Institute for Advanced Biosciences, Keio University.<br /> | |
54 The original web service is located at the following URL:<br /> | |
55 <br /> | |
56 http://www.g-language.org/wiki/soap<br /> | |
57 <br /> | |
58 WSDL(RPC/Encoded) file is located at:<br /> | |
59 <br /> | |
60 http://soap.g-language.org/g-language.wsdl<br /> | |
61 <br /> | |
62 Documentation on G-language Genome Analysis Environment methods are<br /> | |
63 provided at the Document Center<br /> | |
64 <br /> | |
65 http://ws.g-language.org/gdoc/<br /> | |
66 <br /> | |
67 | |
68 </p> | |
69 | |
70 <H2>Usage</H2> | |
71 | |
72 Here is a sample session with gdeltagcskew | |
73 | |
74 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> | |
75 | |
76 % gdeltagcskew refseqn:NC_000913 | |
77 Calculate strand bias of bacterial genome using delta GC skew index | |
78 Program compseq output file [nc_000913.gdeltagcskew]: | |
79 | |
80 </pre></td></tr></table> | |
81 | |
82 Go to the <a href="#input">input files</a> for this example<br> | |
83 Go to the <a href="#output">output files</a> for this example<br><br> | |
84 | |
85 <h2>Command line arguments</h2> | |
86 | |
87 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> | |
88 <tr bgcolor="#FFFFCC"> | |
89 <th align="left">Qualifier</th> | |
90 <th align="left">Type</th> | |
91 <th align="left">Description</th> | |
92 <th align="left">Allowed values</th> | |
93 <th align="left">Default</th> | |
94 </tr> | |
95 | |
96 <tr bgcolor="#FFFFCC"> | |
97 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> | |
98 </tr> | |
99 | |
100 <tr bgcolor="#FFFFCC"> | |
101 <td>[-sequence]<br>(Parameter 1)</td> | |
102 <td>seqall</td> | |
103 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> | |
104 <td>Readable sequence(s)</td> | |
105 <td><b>Required</b></td> | |
106 </tr> | |
107 | |
108 <tr bgcolor="#FFFFCC"> | |
109 <td>[-outfile]<br>(Parameter 2)</td> | |
110 <td>outfile</td> | |
111 <td>Program compseq output file</td> | |
112 <td>Output file</td> | |
113 <td><i><*></i>.gdeltagcskew</td> | |
114 </tr> | |
115 | |
116 <tr bgcolor="#FFFFCC"> | |
117 <th align="left" colspan=5>Additional (Optional) qualifiers</th> | |
118 </tr> | |
119 | |
120 <tr> | |
121 <td colspan=5>(none)</td> | |
122 </tr> | |
123 | |
124 <tr bgcolor="#FFFFCC"> | |
125 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> | |
126 </tr> | |
127 | |
128 <tr bgcolor="#FFFFCC"> | |
129 <td>-at</td> | |
130 <td>boolean</td> | |
131 <td>Include when observing AT skew instead of GC skew</td> | |
132 <td>Boolean value Yes/No</td> | |
133 <td>No</td> | |
134 </tr> | |
135 | |
136 <tr bgcolor="#FFFFCC"> | |
137 <td>-purine</td> | |
138 <td>boolean</td> | |
139 <td>Include when observing purine (AG/TC) skew</td> | |
140 <td>Boolean value Yes/No</td> | |
141 <td>No</td> | |
142 </tr> | |
143 | |
144 <tr bgcolor="#FFFFCC"> | |
145 <td>-keto</td> | |
146 <td>boolean</td> | |
147 <td>Include when observing keto (TG/AC) skew</td> | |
148 <td>Boolean value Yes/No</td> | |
149 <td>No</td> | |
150 </tr> | |
151 | |
152 <tr bgcolor="#FFFFCC"> | |
153 <td>-method</td> | |
154 <td>selection</td> | |
155 <td>Choose the nucleotides to use 'degenerate', 'gc3', or 'all'</td> | |
156 <td>Choose from selection list of values</td> | |
157 <td>degenerate</td> | |
158 </tr> | |
159 | |
160 <tr bgcolor="#FFFFCC"> | |
161 <td>-[no]accid</td> | |
162 <td>boolean</td> | |
163 <td>Include to use sequence accession ID as query</td> | |
164 <td>Boolean value Yes/No</td> | |
165 <td>Yes</td> | |
166 </tr> | |
167 | |
168 </table> | |
169 | |
170 | |
171 <h2 id="input">Input file format</h2> | |
172 | |
173 <p> | |
174 The database definitions for following commands are available at<br /> | |
175 http://soap.g-language.org/kbws/embossrc<br /> | |
176 <br /> | |
177 gdeltagcskew reads one or more nucleotide sequences.<br /> | |
178 <br /> | |
179 | |
180 </p> | |
181 | |
182 <h2 id="output">Output file format</h2> | |
183 | |
184 <p> | |
185 The output from gdeltagcskew is to a plain text file.<br /> | |
186 <br /> | |
187 File: nc_000913.gdeltagcskew<br /> | |
188 <br /> | |
189 <table width="90%"><tr><td bgcolor="#CCFFCC"> | |
190 Sequence: NC_000913 DELTA-GCskew -0.108937<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 Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial | |
211 Genomes, Molecular Biology and Evolution, 18(9):1789-1799 | |
212 | |
213 Rocha EPC et al. (2006) Similar compositional biases are caused by very | |
214 different mutational effects, Genome Research, 16:1537-1547 | |
215 | |
216 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and | |
217 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench | |
218 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. | |
219 | |
220 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for | |
221 large-scale analysis of high-throughput omics data, J. Pest Sci., | |
222 31, 7. | |
223 | |
224 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome | |
225 Analysis Environment with REST and SOAP Web Service Interfaces, | |
226 Nucleic Acids Res., 38, W700-W705. | |
227 | |
228 </pre> | |
229 | |
230 <h2>Warnings</h2> | |
231 | |
232 <p> | |
233 None. | |
234 </p> | |
235 | |
236 <h2>Diagnostic Error Messages</h2> | |
237 | |
238 <p> | |
239 None. | |
240 </p> | |
241 | |
242 <h2>Exit status</h2> | |
243 | |
244 <p> | |
245 It always exits with a status of 0. | |
246 </p> | |
247 | |
248 <h2>Known bugs</h2> | |
249 | |
250 <p> | |
251 None. | |
252 </p> | |
253 | |
254 <h2>See also</h2> | |
255 | |
256 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> | |
257 <th>Description</th></tr> | |
258 | |
259 <tr> | |
260 <td><a href="gb1.html">gb1</a></td> | |
261 <td>Calculate strand bias of bacterial genome using B1 index</td> | |
262 </tr><tr> | |
263 <td><a href="gb2.html">gb2</a></td> | |
264 <td>Calculate strand bias of bacterial genome using B2 index</td> | |
265 </tr><tr> | |
266 <td><a href="ggcsi.html">ggcsi</a></td> | |
267 <td>GC Skew Index: an index for strand-specefic mutational bias</td> | |
268 </tr><tr> | |
269 <td><a href="gldabias.html">glda_bias</a></td> | |
270 <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td> | |
271 </tr> | |
272 | |
273 </table> | |
274 | |
275 <h2>Author(s)</h2> | |
276 | |
277 <pre> | |
278 Hidetoshi Itaya (celery@g-language.org) | |
279 Institute for Advanced Biosciences, Keio University | |
280 252-0882 Japan | |
281 | |
282 Kazuharu Arakawa (gaou@sfc.keio.ac.jp) | |
283 Institute for Advanced Biosciences, Keio University | |
284 252-0882 Japan</pre> | |
285 | |
286 <h2>History</h2> | |
287 | |
288 2012 - Written by Hidetoshi Itaya | |
289 | |
290 <h2>Target users</h2> | |
291 | |
292 This program is intended to be used by everyone and everything, from | |
293 naive users to embedded scrips. | |
294 | |
295 <h2>Comments</h2> | |
296 | |
297 None. | |
298 | |
299 </BODY> | |
300 </HTML> |