Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/doc/html/gnucleotideperiodicity.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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| -1:000000000000 | 0:8300eb051bea |
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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> | |
| 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><*></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> |