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| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:20:29 -0400 |
| parents | 8300eb051bea |
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<!--START OF HEADER - DON'T ALTER --> <HTML> <HEAD> <TITLE> EMBOSS: gaaui </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"> gaaui </font></b> </td></tr> </table> <br> <p> <!--END OF HEADER--> <H2> Function </H2> Calculates various indece of amino acid usage <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> gaaui calculates amino acid usage indices for proteins (excluding<br /> formylmethionine). Calculated indices are as follows,<br /> Laa: Length in amino acids<br /> ndaa: Number of different amino acids<br /> Haau: Entropy of amino acid usage<br /> mmw: Mean molecular weight<br /> gravy: Mean hydropathic indices of each amino acid<br /> aroma: Relative frequency of aromatic amino acids<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 gaaui <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gaaui refseqn:NC_000913 Calculates various indece of amino acid usage AAINDEX entry output file [nc_000913.gaaui]: </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>AAINDEX entry output file</td> <td>Output file</td> <td><i><*></i>.gaaui</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 /> gaaui reads one or more nucleotide sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gaaui is to a plain text file.<br /> <br /> File: nc_000913.gaaui<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: NC_000913<br /> Laa,ndaa,Haau,mmw,gravy,aroma,gene<br /> 20,8,2.4842,117.48,+0.0150,0.0000,thrL<br /> 819,20,4.0887,126.65,+0.0328,0.0659,thrA<br /> 309,20,4.1228,126.35,+0.0181,0.0712,thrB<br /> 427,20,4.0806,128.00,-0.1014,0.0843,thrC<br /> 97,18,3.9165,133.54,-1.0268,0.0928,yaaX<br /> 257,19,4.0733,132.55,-0.4117,0.1089,yaaA<br /> 475,20,4.0413,126.46,+0.6781,0.1242,yaaJ<br /> 316,20,4.0395,128.99,-0.2165,0.0728,talB<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> 169,20,4.0001,124.90,+0.0231,0.0710,yjjX<br /> 214,20,3.9937,129.77,-0.3813,0.0374,ytjC<br /> 288,20,4.1421,132.58,-0.3628,0.1111,rob<br /> 156,20,4.0627,126.72,-0.0442,0.0705,creA<br /> 228,20,4.0471,131.94,-0.1408,0.0789,creB<br /> 473,20,4.0254,128.01,+0.0023,0.0677,creC<br /> 449,20,4.0871,128.66,+0.2082,0.0980,creD<br /> 237,20,4.0729,132.54,-0.4970,0.0675,arcA<br /> 45,15,3.5800,123.27,+0.7533,0.0222,yjjY<br /> 227,20,4.0283,128.63,-0.0031,0.0573,yjtD<br /> </td></tr></table> <br /> <br /> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Lobry, JR. and Gautier, C. (1994) Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes, Nucleic Acids Res, 22:3174-3180.a Zavala A et al. (2002) Trends in codon and amino acid usage in Thermotoga maritima J Mol Evol. 54(5):563-8. 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="gaminoinfo.html">gaminoinfo</a></td> <td>Prints out basic amino acid sequence statistics</td> </tr><tr> <td><a href="gcodoncompiler.html">gcodoncompiler</a></td> <td>Calculate various kinds of amino acid and codon usage data</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.