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<TITLE> EMBOSS: gshuffleseq </TITLE>
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<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>
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gshuffleseq
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<H2> Function </H2>
Create randomized sequence with conserved k-mer composition
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<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>
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<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>
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<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
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<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>
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<td>[-outseq]<br>(Parameter 2)</td>
<td>seqout</td>
<td>Sequence filename and optional format (output USA)</td>
<td>Writeable sequence</td>
<td><i><*></i>.<i>format</i></td>
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<th align="left" colspan=5>Additional (Optional) qualifiers</th>
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<td colspan=5>(none)</td>
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<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
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<td>-k</td>
<td>integer</td>
<td>Sequence k-mer to preserve composition</td>
<td>Any integer value</td>
<td>1</td>
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<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 />
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<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>
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<td><a href="shuffleseq.html">shuffleseq</a></td>
<td>Shuffles a set of sequences maintaining composition</td>
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<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.
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