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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gbasecounter </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 gbasecounter
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 Creates a position weight matrix of oligomers around start codon
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 This function creates a position weight matrix (PWM) of<br />
45 oligomers of specified length around the start codon of all<br />
46 genes in the given genome.<br />
47 <br />
48 G-language SOAP service is provided by the<br />
49 Institute for Advanced Biosciences, Keio University.<br />
50 The original web service is located at the following URL:<br />
51 <br />
52 http://www.g-language.org/wiki/soap<br />
53 <br />
54 WSDL(RPC/Encoded) file is located at:<br />
55 <br />
56 http://soap.g-language.org/g-language.wsdl<br />
57 <br />
58 Documentation on G-language Genome Analysis Environment methods are<br />
59 provided at the Document Center<br />
60 <br />
61 http://ws.g-language.org/gdoc/<br />
62 <br />
63
64 </p>
65
66 <H2>Usage</H2>
67
68 Here is a sample session with gbasecounter
69
70 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
71
72 % gbasecounter refseqn:NC_000913
73 Creates a position weight matrix of oligomers around start codon
74 Weight matrix output file [nc_000913.gbasecounter]:
75
76 </pre></td></tr></table>
77
78 Go to the <a href="#input">input files</a> for this example<br>
79 Go to the <a href="#output">output files</a> for this example<br><br>
80
81 <h2>Command line arguments</h2>
82
83 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
84 <tr bgcolor="#FFFFCC">
85 <th align="left">Qualifier</th>
86 <th align="left">Type</th>
87 <th align="left">Description</th>
88 <th align="left">Allowed values</th>
89 <th align="left">Default</th>
90 </tr>
91
92 <tr bgcolor="#FFFFCC">
93 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
94 </tr>
95
96 <tr bgcolor="#FFFFCC">
97 <td>[-sequence]<br>(Parameter 1)</td>
98 <td>seqall</td>
99 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
100 <td>Readable sequence(s)</td>
101 <td><b>Required</b></td>
102 </tr>
103
104 <tr bgcolor="#FFFFCC">
105 <td>[-outfile]<br>(Parameter 2)</td>
106 <td>outfile</td>
107 <td>Weight matrix output file</td>
108 <td>Output file</td>
109 <td><i>&lt;*&gt;</i>.gbasecounter</td>
110 </tr>
111
112 <tr bgcolor="#FFFFCC">
113 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
114 </tr>
115
116 <tr>
117 <td colspan=5>(none)</td>
118 </tr>
119
120 <tr bgcolor="#FFFFCC">
121 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
122 </tr>
123
124 <tr bgcolor="#FFFFCC">
125 <td>-position</td>
126 <td>selection</td>
127 <td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td>
128 <td>Choose from selection list of values</td>
129 <td>start</td>
130 </tr>
131
132 <tr bgcolor="#FFFFCC">
133 <td>-patlen</td>
134 <td>integer</td>
135 <td>Length of oligomer to count</td>
136 <td>Any integer value</td>
137 <td>3</td>
138 </tr>
139
140 <tr bgcolor="#FFFFCC">
141 <td>-upstream</td>
142 <td>integer</td>
143 <td>Length upstream of specified position to create PWM</td>
144 <td>Any integer value</td>
145 <td>30</td>
146 </tr>
147
148 <tr bgcolor="#FFFFCC">
149 <td>-downstream</td>
150 <td>integer</td>
151 <td>Length downstream of specified position to create PWM</td>
152 <td>Any integer value</td>
153 <td>30</td>
154 </tr>
155
156 <tr bgcolor="#FFFFCC">
157 <td>-[no]accid</td>
158 <td>boolean</td>
159 <td>Include to use sequence accession ID as query</td>
160 <td>Boolean value Yes/No</td>
161 <td>Yes</td>
162 </tr>
163
164 </table>
165
166
167 <h2 id="input">Input file format</h2>
168
169 <p>
170 The database definitions for following commands are available at<br />
171 http://soap.g-language.org/kbws/embossrc<br />
172 <br />
173 gbasecounter reads one or more nucleotide sequences.<br />
174 <br />
175
176 </p>
177
178 <h2 id="output">Output file format</h2>
179
180 <p>
181 The output from gbasecounter is to a plain text file.<br />
182 <br />
183 File: nc_000913.gbasecounter<br />
184 <br />
185 <table width="90%"><tr><td bgcolor="#CCFFCC">
186 Sequence: NC_000913<br />
187 Pattern,30,29,28,27,26,25,24,23,22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0,-1,-2,-3,-4,-5,-6,-7,-8,-9,-10,-11,-12,-13,-14,-15,-16,-17,-18,-19,-20,-21,-22,-23,-24,-25,-26,-27,-28,-29,-30<br />
188 aaa,0,1,199,111,104,139,94,103,99,44,42,26,75,103,107,95,107,103,102,82,91,71,73,81,86,80,74,74,78,65,69,65,31,41,68,51,61,83,55,67,92,55,71,89,60,77,100,59,87,123,97,105,141,83,117,180,154,203,262,2,0<br />
189 aac,2,0,0,63,104,56,67,64,28,34,22,12,17,37,43,59,61,71,54,42,62,59,63,52,56,61,48,55,56,52,38,30,34,54,36,42,43,33,49,49,36,43,58,37,53,62,46,47,79,38,52,72,58,52,89,74,83,91,68,2,1<br />
190 aag,0,0,17,46,38,57,56,44,25,44,43,170,162,125,92,70,61,50,42,46,21,22,43,39,29,35,39,34,28,26,30,25,9,43,31,12,55,33,13,66,21,21,50,30,21,55,31,21,47,38,16,55,35,23,63,96,31,51,71,0,0<br />
191 aat,1,565,4,56,124,45,83,74,63,42,24,24,20,27,59,71,54,74,66,71,67,52,58,77,61,52,57,49,56,71,61,34,33,24,40,38,30,43,46,25,48,56,35,58,51,33,47,71,46,70,77,60,74,74,73,83,69,61,110,0,1<br />
192 aca,0,1,92,73,39,69,39,24,31,31,16,19,34,64,61,63,65,56,42,60,45,66,38,45,46,41,49,40,51,43,39,20,34,29,23,26,28,34,35,26,35,39,30,28,48,26,28,53,35,36,59,42,53,46,64,56,62,44,55,0,0<br />
193 acc,2,2,0,81,37,19,28,19,15,8,12,7,7,14,22,27,30,24,31,23,30,27,34,27,30,22,25,42,34,29,25,41,23,32,44,19,32,51,21,19,50,23,24,52,30,31,56,25,31,55,30,25,35,30,32,53,20,21,48,0,2<br />
194 acg,0,0,21,38,23,38,32,25,13,18,12,15,34,29,34,37,25,31,25,34,30,20,22,24,40,22,24,30,34,29,25,29,25,34,41,23,32,25,36,44,28,32,40,32,23,28,40,30,25,36,39,32,28,40,38,39,45,30,33,0,0<br />
195 act,0,0,1,57,35,14,30,29,21,9,6,9,9,10,17,38,28,35,30,37,41,46,38,43,39,31,31,31,30,32,27,18,55,24,20,32,16,25,32,24,31,44,14,33,43,12,35,60,24,40,58,19,36,71,22,44,46,13,45,3,1<br />
196 <br />
197 <font color=red>[Part of this file has been deleted for brevity]</font><br />
198 <br />
199 tcg,0.000,0.000,0.347,0.255,0.301,0.764,0.347,0.232,0.162,0.093,0.093,0.278,0.347,0.370,0.370,0.440,0.556,0.394,0.486,0.440,0.417,0.347,0.370,0.463,0.417,0.695,0.394,0.671,0.533,0.579,0.602,0.347,0.695,1.598,0.556,0.648,1.366,0.394,0.463,1.505,0.579,0.810,1.320,0.278,0.810,1.065,0.533,0.579,0.972,0.255,0.787,1.158,0.440,0.787,0.602,0.255,0.625,0.463,0.347,0.000,0.000<br />
200 tct,0.000,0.046,0.000,0.671,0.764,0.394,0.278,0.347,0.278,0.116,0.116,0.162,0.255,0.162,0.486,0.648,0.533,0.625,0.741,0.718,0.903,0.834,0.880,0.857,0.741,0.857,0.671,0.648,0.857,0.695,0.625,0.440,0.880,0.463,0.556,1.111,0.509,0.579,1.227,0.556,0.370,1.135,0.671,0.648,1.250,0.834,0.509,1.273,0.440,0.718,0.972,1.042,0.648,0.926,0.533,0.625,0.556,0.185,1.690,0.000,0.000<br />
201 tga,0.000,0.000,2.315,0.463,1.227,1.297,1.088,0.949,0.625,0.417,1.065,0.903,1.737,1.667,1.042,1.158,1.366,1.320,1.227,1.158,0.926,1.459,1.181,0.810,1.366,0.972,0.972,1.111,0.764,0.787,1.227,0.000,1.598,1.250,0.000,1.482,1.181,0.000,1.459,1.389,0.000,1.783,1.297,0.000,1.505,1.482,0.023,1.343,1.690,0.000,1.690,1.204,0.000,1.389,0.949,0.000,2.408,0.996,0.000,0.023,24.311<br />
202 tgc,0.023,0.000,0.000,0.394,0.996,0.579,0.787,0.556,0.208,0.185,0.208,0.116,0.278,0.324,0.394,0.834,0.486,0.394,0.718,0.556,0.509,0.857,0.509,0.625,0.810,0.741,0.695,0.834,0.625,0.787,1.158,0.347,1.158,1.621,0.394,1.667,1.204,0.347,1.551,1.320,0.417,1.088,1.065,0.232,1.320,1.042,0.139,1.204,0.996,0.208,0.996,0.602,0.139,0.648,0.764,0.069,0.857,0.394,0.023,0.000,7.803<br />
203 tgg,0.000,0.023,0.069,0.208,0.370,0.509,0.486,0.417,0.394,0.671,1.343,1.713,1.621,1.482,0.810,0.834,0.718,0.301,0.463,0.509,0.509,0.741,0.579,0.509,0.625,0.486,0.509,0.625,0.625,0.533,0.857,0.996,0.718,1.968,1.042,0.880,1.760,0.671,0.949,1.459,0.556,0.787,0.903,0.718,0.695,1.273,0.533,0.440,0.648,0.880,0.417,0.718,0.648,0.278,0.625,0.463,0.440,0.486,0.116,0.023,11.021<br />
204 tgt,0.023,0.880,0.023,0.533,1.135,0.301,0.440,0.602,0.417,0.208,0.232,0.185,0.185,0.278,0.370,0.440,0.533,0.556,0.648,0.764,0.509,0.926,0.579,0.718,0.880,0.695,0.718,0.741,0.741,0.579,0.625,0.278,1.158,0.857,0.278,0.972,0.718,0.324,0.926,0.695,0.463,1.111,0.834,0.162,1.482,0.787,0.278,1.065,0.695,0.278,1.042,0.695,0.208,0.903,0.718,0.139,0.857,0.232,0.093,0.023,7.340<br />
205 tta,0.000,0.000,6.506,0.648,0.810,1.829,1.320,0.602,0.486,0.509,0.255,0.347,0.301,0.834,1.320,1.459,1.412,1.667,1.644,1.852,1.667,1.574,1.366,1.042,1.204,1.621,1.505,1.227,1.436,1.088,1.273,1.343,0.486,1.158,1.042,0.440,1.135,1.389,0.370,1.273,1.574,0.486,1.875,1.505,0.463,1.991,1.875,0.533,2.362,2.061,0.324,2.084,2.200,0.509,1.505,1.320,0.463,1.366,0.648,0.000,0.069<br />
206 ttc,0.000,0.000,0.000,0.648,0.417,0.695,0.764,0.347,0.301,0.278,0.208,0.023,0.232,0.533,0.718,0.718,0.903,1.042,1.158,0.880,1.158,1.065,0.903,0.834,1.343,0.996,0.926,0.810,0.741,0.834,1.042,0.926,0.579,1.088,0.695,0.695,1.297,0.741,0.741,1.111,0.926,0.787,1.366,0.695,0.857,1.412,0.648,0.834,1.111,0.440,0.602,1.250,1.019,1.135,0.787,0.440,0.880,0.509,0.370,0.000,0.000<br />
207 ttg,0.857,0.023,0.255,0.394,0.556,1.111,0.533,0.463,0.417,0.185,0.232,0.533,0.602,1.042,0.718,0.695,1.135,0.972,0.857,0.926,0.787,0.671,1.320,0.695,0.903,1.204,0.880,0.764,0.926,0.741,0.718,1.019,0.347,1.551,1.042,0.370,2.014,0.834,0.463,2.061,0.880,0.278,2.014,0.857,0.208,2.593,0.741,0.278,1.922,0.764,0.417,2.130,0.834,0.208,1.111,0.394,0.093,1.111,0.417,0.000,0.023<br />
208 ttt,0.023,0.440,0.093,1.598,1.181,1.320,1.829,1.343,0.648,0.370,0.394,0.278,0.185,0.440,1.135,1.574,1.667,1.945,2.315,2.362,2.431,2.501,2.107,2.362,1.806,2.014,2.292,2.014,1.598,1.760,1.829,1.389,1.505,1.042,1.343,1.297,0.926,1.528,1.574,1.227,1.482,1.737,1.389,1.667,1.922,1.389,1.945,1.922,1.343,1.806,1.760,1.389,2.014,1.760,1.065,0.949,1.111,0.625,1.227,0.023,0.023<br />
209 </td></tr></table>
210
211 </p>
212
213 <h2>Data files</h2>
214
215 <p>
216 None.
217 </p>
218
219 <h2>Notes</h2>
220
221 <p>
222 None.
223 </p>
224
225 <h2>References</h2>
226
227 <pre>
228 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
229 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
230 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
231
232 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
233 large-scale analysis of high-throughput omics data, J. Pest Sci.,
234 31, 7.
235
236 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
237 Analysis Environment with REST and SOAP Web Service Interfaces,
238 Nucleic Acids Res., 38, W700-W705.
239
240 </pre>
241
242 <h2>Warnings</h2>
243
244 <p>
245 None.
246 </p>
247
248 <h2>Diagnostic Error Messages</h2>
249
250 <p>
251 None.
252 </p>
253
254 <h2>Exit status</h2>
255
256 <p>
257 It always exits with a status of 0.
258 </p>
259
260 <h2>Known bugs</h2>
261
262 <p>
263 None.
264 </p>
265
266 <h2>See also</h2>
267
268 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
269 <th>Description</th></tr>
270
271 <tr>
272 <td><a href="gbasezvalue.html">gbasezvalue</a></td>
273 <td>Extracts conserved oligomers per position using Z-score</td>
274 </tr><tr>
275 <td><a href="gviewcds.html">gviewcds</a></td>
276 <td>Displays a graph of nucleotide contents around start and stop codons</td>
277 </tr>
278
279 </table>
280
281 <h2>Author(s)</h2>
282
283 <pre>
284 Hidetoshi Itaya (celery@g-language.org)
285 Institute for Advanced Biosciences, Keio University
286 252-0882 Japan
287
288 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
289 Institute for Advanced Biosciences, Keio University
290 252-0882 Japan</pre>
291
292 <h2>History</h2>
293
294 2012 - Written by Hidetoshi Itaya
295
296 <h2>Target users</h2>
297
298 This program is intended to be used by everyone and everything, from
299 naive users to embedded scrips.
300
301 <h2>Comments</h2>
302
303 None.
304
305 </p>
306
307 </BODY>
308 </HTML>