Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/html/gaminoinfo.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/gaminoinfo.html Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,1 @@ +<!--START OF HEADER - DON'T ALTER --> <HTML> <HEAD> <TITLE> EMBOSS: gaminoinfo </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"> gaminoinfo </font></b> </td></tr> </table> <br> <p> <!--END OF HEADER--> <H2> Function </H2> Prints out basic amino acid sequence statistics <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> gaminoinfo prints out basic compositional statistics of the given amino<br /> acid sequence in a human readble manner. The calculated values are molecular<br /> weight, number of residues, average residue weight, charge, isoelectric<br /> point, number/mole/Dayhoffstat of each amino acid, and percentage of<br /> Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V), Aliphatic (I+L+V),<br /> Armoatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),<br /> Polar (D+E+H+K+N+Q+R+S+T+Z), Charged (B+D+E+H+K+R+Z), Basic (H+K+R), and<br /> Acidic (B+D+E+Z) reidues.<br /> <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 gaminoinfo <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gaminoinfo tsw:hbb_human Prints out basic amino acid sequence statistics AAINDEX entry output file [hbb_human.gaminoinfo]: </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>Protein 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>.gaminoinfo</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> <td colspan=5>(none)</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 /> gaminoinfo reads one or more protein sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gaminoinfo is to a plain text file.<br /> <br /> File: hbb_human.gaminoinfo<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> Sequence: P68871<br /> AminoInfo of from 1 to 158<br /> <br /> Molecular weight = 19309.27 Residues = 158<br /> Average Weight = 122.21 Charge = 3.5<br /> Isoelectric Point = 7.4065<br /> Residue Number Mole% DayhoffStat<br /> <br /> = 1 0.633 0.000<br /> > = 1 0.633 0.000<br /> A = Ala 16 10.127 1.178<br /> B = Asx 2 1.266 0.000<br /> C = Cys 2 1.266 0.436<br /> D = Asp 7 4.430 0.806<br /> E = Glu 8 5.063 0.844<br /> F = Phe 8 5.063 1.406<br /> G = Gly 13 8.228 0.980<br /> H = His 11 6.962 3.481<br /> K = Lys 11 6.962 1.055<br /> L = Leu 18 11.392 1.540<br /> M = Met 3 1.899 1.117<br /> N = Asn 7 4.430 1.030<br /> P = Pro 7 4.430 0.852<br /> Q = Gln 3 1.899 0.487<br /> R = Arg 3 1.899 0.387<br /> S = Ser 5 3.165 0.452<br /> T = Thr 7 4.430 0.726<br /> U = Sec 1 0.633 0.000<br /> V = Val 18 11.392 1.726<br /> W = Trp 2 1.266 0.974<br /> Y = Tyr 3 1.899 0.558<br /> _ = 1 0.633 0.000<br /> <br /> Property Residues Number Mole%<br /> Tiny (A+C+G+S+T) 43 27.215<br /> Small (A+B+C+D+G+N+P+S+T+V) 84 53.165<br /> Aliphatic (I+L+V) 36 22.785<br /> Aromatic (F+H+W+Y) 24 15.190<br /> Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 90 56.962<br /> Polar (D+E+H+K+N+Q+R+S+T+Z) 62 39.241<br /> Charged (B+D+E+H+K+R+Z) 42 26.582<br /> Basic (H+K+R) 25 15.823<br /> Acidic (B+D+E+Z) 17 10.759<br /> </pre></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="gaaui.html">gaaui</a></td> <td>Calculates various indece of amino acid usage</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. \ No newline at end of file