annotate GEMBASSY-1.0.3/doc/html/gshuffleseq.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: gshuffleseq </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"> gshuffleseq </font></b> </td></tr> </table> <br>&nbsp; <p> <!--END OF HEADER--> <H2> Function </H2> Create randomized sequence with conserved k-mer composition <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> gshuffleseq shuffles and randomizes the given sequence, conserving the<br /> nucleotide/peptide k-mer content of the original sequence.<br /> <br /> For k=1, i.e. shuffling sequencing preserving single nucleotide composition,<br /> Fisher-Yates Algorithm is employed.<br /> For k>1, shuffling preserves all k-mers (all k where k=1~k). For example,<br /> k=3 preserves all triplet, doublet, and single nucleotide composition.<br /> Algorithm for k-mer preserved shuffling is non-trivial, which is solved<br /> by graph theoretical approach with Eulerian random walks in the graph of<br /> k-1-mers. See Jiang et al., Kandel et al., and Propp et al., for details<br /> of this algorithm.<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 gshuffleseq <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % gshuffleseq tsw:hbb_human Create randomized sequence with conserved k-mer composition output sequence [hbb_human.fasta]: </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>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>[-outseq]<br>(Parameter 2)</td> <td>seqout</td> <td>Sequence filename and optional format (output USA)</td> <td>Writeable sequence</td> <td><i>&lt;*&gt;</i>.<i>format</i></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>-k</td> <td>integer</td> <td>Sequence k-mer to preserve composition</td> <td>Any integer value</td> <td>1</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 /> gshuffleseq reads one or more nucleotide or protein sequences.<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> The output from gshuffleseq is to .<br /> <br /> File: hbb_human.fasta<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> >HBB_HUMAN P68871 Hemoglobin subunit beta (Beta-globin) (Hemoglobin beta chain) (LVV-hemorphin-7)<br /> KGWLDLVAGAAHFVRRLKMLLEVDWAAHEERVGTSNPNNALKNEAADVEVHSPTHVNPTQ<br /> LVLVQVGFGTLHLQGVECPKPKPGGVALKPVAHLLAMKECTLVALGSDFYVDHGSDGEDK<br /> GFKAYVLATSFFAYTNFLHGKVKHVLF<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Fisher R.A. and Yates F. (1938) "Example 12", Statistical Tables, London Durstenfeld R. (1964) "Algorithm 235: Random permutation", CACM 7(7):420 Jiang M., Anderson J., Gillespie J., and Mayne M. (2008) "uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts", BMC Bioinformatics 9:192 Kandel D., Matias Y., Unver R., and Winker P. (1996) "Shuffling biological sequences", Discrete Applied Mathematics 71(1-3):171-185 Propp J.G. and Wilson D.B. (1998) "How to get a perfectly random sample from a generic Markov chain and generate a random spanning tree of a directed graph", Journal of Algorithms 27(2):170-217 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="shuffleseq.html">shuffleseq</a></td> <td>Shuffles a set of sequences maintaining composition</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>