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1 <!--START OF HEADER - DON'T ALTER --> <HTML> <HEAD> <TITLE> EMBOSS: gicdi </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"> gicdi </font></b> </td></tr> </table> <br>&nbsp; <p> <!--END OF HEADER--> <H2> Function </H2> Calculates the intrinsic codon deviation index (ICDI) <!-- 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 gicdi <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gicdi refseqn:NC_000913 Calculates the intrinsic codon deviation index (ICDI) Codon usage output file [nc_000913.gicdi]: </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>.gicdi</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 /> gicdi reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gicdi is to a plain text file.<br /> <br /> File: nc_000913.gicdi<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> icdi,gene<br /> 0.8192,thrL<br /> 0.1258,thrA<br /> 0.1127,thrB<br /> 0.1689,thrC<br /> 0.3099,yaaX<br /> 0.2030,yaaA<br /> 0.1600,yaaJ<br /> 0.3533,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 0.2203,yjjX<br /> 0.2719,ytjC<br /> 0.1377,rob<br /> 0.2647,creA<br /> 0.1944,creB<br /> 0.1733,creC<br /> 0.1926,creD<br /> 0.2728,arcA<br /> 0.5171,yjjY<br /> 0.2434,yjtD<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon usage bias, J Mol Evol, 47(3):268-74. Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes, Gene, 139:43-49. 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="gcbi.html">gcbi</a></td> <td>Calculates the codon bias index (CBI)</td> </tr><tr> <td><a href="gdeltaenc.html">gdelta_enc</a></td> <td>Calculate the codon usage bias related to translation optimization (delta ENC)</td> </tr><tr> <td><a href="gsvalue.html">gs_value</a></td> <td>Calculate the strength of selected codon usage bias (S)</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>