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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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<!--START OF HEADER - DON'T ALTER --> <HTML> <HEAD> <TITLE> EMBOSS: ggeneskew </TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" text="#000000"> <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <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> </td> <td align=left valign=middle> <b><font size="+6"> ggeneskew </font></b> </td></tr> </table> <br> <p> <!--END OF HEADER--> <H2> Function </H2> Calculate the gene strand bias of the given genome <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> ggeneskew calculates and plots the strand bias of genes (or the GC skew<br /> within them). By default, this program visualizes the gene strand preference<br /> (1 for direct, -1 for complement strand), but by specifying -base option<br /> option, GC/AT/Purine/Keto skews of the coding regions or more specifically<br /> in the GC3 (third codon position) with -gctri option can be calculated.<br /> <br /> G-language SOAP service is provided by the<br /> Institute for Advanced Biosciences, Keio University.<br /> The original web service is located at the following URL:<br /> <br /> http://www.g-language.org/wiki/soap<br /> <br /> WSDL(RPC/Encoded) file is located at:<br /> <br /> http://soap.g-language.org/g-language.wsdl<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with ggeneskew <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggeneskew refseqn:NC_000913 Calculate the gene strand bias of the given genome Program compseq output file (optional) [nc_000913.ggeneskew]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % ggeneskew refseqn:NC_000913 -plot -graph png Calculate the gene strand bias of the given genome Created ggeneskew.1.png </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>-graph</td> <td>xygraph</td> <td>Graph type</td> <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> <td><i>EMBOSS_GRAPHICS</i> value, or x11</td> </tr> <tr bgcolor="#FFFFCC"> <td>-outfile</td> <td>outfile</td> <td>Program compseq output file (optional)</td> <td>Output file</td> <td><i><*></i>.ggeneskew</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-window</td> <td>integer</td> <td>Window size to observe</td> <td>Any integer value</td> <td>10000</td> </tr> <tr bgcolor="#FFFFCC"> <td>-slide</td> <td>integer</td> <td>Window slide size</td> <td>Any integer value</td> <td>10000</td> </tr> <tr bgcolor="#FFFFCC"> <td>-cumulative</td> <td>boolean</td> <td>Input 1 to calculate cumulative skew</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-base</td> <td>selection</td> <td>Input 'gc', 'at', 'purine', or 'keto' for observing GC/AT/Purine/Keto skews</td> <td>Choose from selection list of values</td> <td>none</td> </tr> <tr bgcolor="#FFFFCC"> <td>-gctri</td> <td>boolean</td> <td>Include to use only the third codon positions</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> <tr bgcolor="#FFFFCC"> <td>-plot</td> <td>toggle</td> <td>Include to plot result</td> <td>Toggle value Yes/No</td> <td>No</td> </tr> </table> <h2 id="input">Input file format</h2> <p> The database definitions for following commands are available at<br /> http://soap.g-language.org/kbws/embossrc<br /> <br /> ggeneskew reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from ggeneskew is to a plain text file or the EMBOSS graphics device.<br /> <br /> File: nc_000913.ggeneskew<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> location,gene None skew<br /> 190,0.294118<br /> 337,-0.058914<br /> 2801,-0.120000<br /> 3734,-0.070588<br /> 5234,0.037500<br /> 5683,0.020725<br /> 6529,0.032765<br /> 8238,-0.028226<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 4631820,-0.093407<br /> 4632464,-0.006479<br /> 4633544,-0.120690<br /> 4634030,-0.060367<br /> 4634719,-0.104167<br /> 4636201,-0.144560<br /> 4637613,0.010929<br /> 4638425,0.200000<br /> 4638965,-0.081871<br /> ,<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="ggcskew.html">ggcskew</a></td> <td>Calculates the GC skew of the input sequence</td> </tr><tr> <td><a href="ggcwin.html">ggcwin</a></td> <td>Calculates the GC content along the given genome</td> </tr><tr> <td><a href="ggenomicskew.html">ggenomicskew</a></td> <td>Calculates the GC skew in different regions of the given genome</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None.