annotate GEMBASSY-1.0.3/doc/html/gphx.html @ 1:84a17b3fad1f draft

Uploaded
author ktnyt
date Fri, 26 Jun 2015 05:20:29 -0400
parents 8300eb051bea
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
1 <!--START OF HEADER - DON'T ALTER --> <HTML> <HEAD> <TITLE> EMBOSS: gphx </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"> gphx </font></b> </td></tr> </table> <br>&nbsp; <p> <!--END OF HEADER--> <H2> Function </H2> Identify predicted highly expressed gene <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> gphx calculates codon usage differences between gene classes for identifying<br /> Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is<br /> identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's<br /> nature. PHX genes are known to generally have favorable codon usage, strong<br /> SD sequences, and probably stronger conservation of promoter sequences.<br /> A gene is idenfitied as PA if BgC and BgH is greater than the median of<br /> BgC for every gene with a length close to the gene.<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 gphx <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gphx refseqn:NC_000913 Identify predicted highly expressed gene Codon usage output file [nc_000913.gphx]: </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>Codon usage output file</td> <td>Output file</td> <td><i>&lt;*&gt;</i>.gphx</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>-translate</td> <td>boolean</td> <td>Include when translating using standard codon table</td> <td>Boolean value Yes/No</td> <td>No</td> </tr> <tr bgcolor="#FFFFCC"> <td>-delkey</td> <td>string</td> <td>Regular expression to delete key</td> <td>Any string</td> <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</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> </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 /> gphx reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gphx is to a plain text file.<br /> <br /> File: nc_000913.gphx<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> BgC,BgH,E_g,phx,pa,gene<br /> 0.8070,0.8977,0.8990,0,1,thrL<br /> 0.1857,0.5958,0.3116,0,0,thrA<br /> 0.2323,0.5964,0.3896,0,0,thrB<br /> 0.2353,0.6064,0.3881,0,0,thrC<br /> 0.4353,0.6020,0.7231,0,1,yaaX<br /> 0.2961,0.6790,0.4361,0,0,yaaA<br /> 0.2233,0.7009,0.3186,0,0,yaaJ<br /> 0.4149,0.3071,1.3511,1,0,talB<br /> <br /> [Part of this file has been deleted for brevity]<br /> <br /> 0.3255,0.7038,0.4625,0,0,yjjX<br /> 0.3531,0.5906,0.5979,0,0,ytjC<br /> 0.2257,0.5235,0.4311,0,0,rob<br /> 0.3584,0.6809,0.5264,0,0,creA<br /> 0.3455,0.7950,0.4346,0,0,creB<br /> 0.2298,0.7154,0.3212,0,0,creC<br /> 0.3299,0.7916,0.4167,0,0,creD<br /> 0.3543,0.3786,0.9357,0,0,arcA<br /> 0.7295,0.8286,0.8804,0,1,yjjY<br /> 0.4028,0.8401,0.4795,0,0,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> CMBL- PHX/PA user guide http://www.cmbl.uga.edu/software/PHX-PA-guide.htm Henry I., Sharp PM. (2007) Predicting gene expression level from codon usage bias Mol Biol Evol, 24(1):10-2. Karlin S., and Mrazek J. (2000) Predicted highly expressed genes of diverse prokaryotic genomes J.Bacteriol, 182(18):5238-5250. 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="gcai.html">gcai</a></td> <td>Calculate codon adaptation index for each gene</td> </tr><tr> <td><a href="gp2.html">gp2</a></td> <td>Calculate the P2 index of each gene</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>