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1 <!--START OF HEADER - DON'T ALTER --> <HTML> <HEAD> <TITLE> EMBOSS: gbui </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"> gbui </font></b> </td></tr> </table> <br>&nbsp; <p> <!--END OF HEADER--> <H2> Function </H2> Calculates base usage indices for protein-coding sequences <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> gbui calculates base usage indices of protein-coding sequences (excluding<br /> start and stop codons) for each gene. Indices calculated are as follows,<br /> acgt: Total bumber of bases (A+T+G+C)<br /> ryr: Purine/Pyrimidine ratio (A+G)/(T+C)<br /> gcc: G+C content (G+C)/(A+T+G+C)<br /> Hgc: entropy of G+C content (G+C)/(A+T+G+C)<br /> gcs: GC skew (C-G)/(C+G)<br /> ats: AT skew (A-T)/(A+T)<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 gbui <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gbui refseqn:NC_000913 Calculates base usage indices for protein-coding sequences Program compseq output file [nc_000913.gbui]: </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>&lt;*&gt;</i>.gbui</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>-position</td> <td>list</td> <td>Codon position</td> <td><table><tr><td>all</td> <td><i>(Assess overall base usage of the gene)</i></td></tr><tr><td>1</td> <td><i>(Assess base usage at 1st position of codons)</i></td></tr><tr><td>2</td> <td><i>(Assess base usage at 2nd position of codons)</i></td></tr><tr><td>3</td> <td><i>(Assess base usage at 3rd position of codons)</i></td></tr></table></td> <td>all</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 /> gbui reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gbui is to a plain text file.<br /> <br /> File: nc_000913.gbui<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> acgt,ryr,gcc,Hgc,gcs,ats,gene<br /> 60,0.9355,0.5333,0.9968,+0.3750,+0.3571,thrL<br /> 2457,1.0206,0.5311,0.9972,-0.0575,-0.0434,thrA<br /> 927,1.0973,0.5653,0.9877,-0.1183,-0.0471,thrB<br /> 1281,1.0795,0.5301,0.9974,-0.0692,+0.0033,thrC<br /> 291,1.0638,0.5430,0.9947,+0.0506,+0.1278,yaaX<br /> 771,1.0615,0.4994,1.0000,-0.0182,+0.0415,yaaA<br /> 1425,0.8363,0.5347,0.9965,-0.0315,-0.2278,yaaJ<br /> 948,1.1303,0.5222,0.9986,-0.0263,+0.0993,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 507,1.0444,0.5661,0.9874,-0.1080,-0.0909,yjjX<br /> 642,1.1472,0.5654,0.9876,-0.0909,+0.0394,ytjC<br /> 864,0.9636,0.5347,0.9965,+0.0087,-0.0299,rob<br /> 468,1.1273,0.4936,0.9999,-0.1169,+0.0042,creA<br /> 684,1.0118,0.5556,0.9911,-0.0579,-0.0592,creB<br /> 1419,1.0655,0.5398,0.9954,-0.1018,-0.0505,creC<br /> 1347,1.0660,0.4974,1.0000,-0.1433,-0.0783,creD<br /> 711,1.0850,0.5134,0.9995,-0.0082,+0.0751,arcA<br /> 135,0.8493,0.4370,0.9885,+0.2203,+0.0263,yjjY<br /> 681,1.1415,0.5007,1.0000,-0.0792,+0.0529,yjtD<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="gdinuc.html">gdinuc</a></td> <td>Calculates dinucleotide usage</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>