Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/html/gb2.html @ 0:8300eb051bea draft
Initial upload
| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEMBASSY-1.0.3/doc/html/gb2.html Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,1 @@ +<!--START OF HEADER - DON'T ALTER --> <HTML> <HEAD> <TITLE> EMBOSS: gb2 </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"> gb2 </font></b> </td></tr> </table> <br> <p> <!--END OF HEADER--> <H2> Function </H2> Calculate strand bias of bacterial genome using B2 index <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> gb2 calculates strand bias of bacterial genome using B2 index,<br /> proposed by Lobry and Sueoka(2002). Basic idea of B2 index is to calculate<br /> the distance from neutral parity state (0.5, 0.5), when the bias of<br /> the coding regions is plotted in a coordinate system with axes representing<br /> G/(G+C) and A/(A+T), using the third codon position of genes. This index<br /> measures the degree of transcription- and translation-associated effects of<br /> bias from Chargaff's second parity rule.<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 gb2 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gb2 refseqn:NC_000913 Calculate strand bias of bacterial genome using B2 index Program compseq output file [nc_000913.gb2]: </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>[-outfile]<br>(Parameter 2)</td> <td>outfile</td> <td>Program compseq output file</td> <td>Output file</td> <td><i><*></i>.gb2</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>-[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> </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 /> gb2 reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gb2 is to a plain text file.<br /> <br /> File: nc_000913.gb2<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913 B2: 0.0919769585775651<br /> </td></tr></table> <br /> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in bacteria, Genome Biology, 3(10):0058 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="gb1.html">gb1</a></td> <td>Calculate strand bias of bacterial genome using B1 index</td> </tr><tr> <td><a href="gdeltagcskew.html">gdeltagcskew</a></td> <td>Calculate strand bias of bacterial genome using delta GC skew</td> </tr><tr> <td><a href="ggcsi.html">ggcsi</a></td> <td>GC Skew Index: an index for strand-specefic mutational bias</td> </tr><tr> <td><a href="gldabias.html">gldabias</a></td> <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</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. </BODY> </HTML> \ No newline at end of file