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<HTML>
<HEAD>
<TITLE>
EMBOSS: shuffleseq
</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="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
shuffleseq
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Shuffles a set of sequences maintaining composition
<H2>
Description
</H2>
This takes a sequence as input and outputs one or more sequences
whose order has been randomly shuffled. No bases or residues
are changed, only their order.
<p>
The number of shuffled sequences output can be set by the
'-shuffle' qualifier.
<H2>
Usage
</H2>
<b>Here is a sample session with shuffleseq</b>
<p>
This makes two randomised copies of the input sequence:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>shuffleseq -shuffle 2 </b>
Shuffles a set of sequences maintaining composition
Input sequence(s): <b>tembl:L48662</b>
output sequence(s) [l48662.fasta]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence(s) filename and optional format, or
reference (input USA)
[-outseq] seqoutall [<sequence>.<format>] Sequence set(s)
filename and optional format (output USA)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-shuffle integer [1] Number of shuffles (Any integer value)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outseq" associated qualifiers
-osformat2 string Output seq format
-osextension2 string File name extension
-osname2 string Base file name
-osdirectory2 string Output directory
-osdbname2 string Database name to add
-ossingle2 boolean Separate file for each entry
-oufo2 string UFO features
-offormat2 string Features format
-ofname2 string Features file name
-ofdirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</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>
<td>[-outseq]<br>(Parameter 2)</td>
<td>Sequence set(s) filename and optional format (output USA)</td>
<td>Writeable sequence(s)</td>
<td><i><*></i>.<i>format</i></td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-shuffle</td>
<td>Number of shuffles</td>
<td>Any integer value</td>
<td>1</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>shuffleseq</b> reads one or more sequence USAs.
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tembl:L48662' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:L48662</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID L48662; SV 1; linear; mRNA; STD; MUS; 366 BP.
XX
AC L48662;
XX
DT 04-NOV-1995 (Rel. 45, Created)
DT 04-MAR-2000 (Rel. 63, Last updated, Version 4)
XX
DE Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy
DE chain mRNA.
XX
KW .
XX
OS Mus musculus (house mouse)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC Muridae; Murinae; Mus.
XX
RN [1]
RP 1-366
RX PUBMED; 8814271.
RA Wloch M.K., Alexander A.L., Pippen A.M., Pisetsky D.S., Gilkeson G.S.;
RT "Differences in V kappa gene utilization and VH CDR3 sequence among
RT anti-DNA from C3H-lpr mice and lupus mice with nephritis";
RL Eur. J. Immunol. 26(9):2225-2233(1996).
XX
DR IMGT/LIGM; L48662; L48662.
XX
FH Key Location/Qualifiers
FH
FT source 1..366
FT /organism="Mus musculus"
FT /strain="C3H/HeJ-lpr/lpr"
FT /mol_type="mRNA"
FT /cell_line="C3H/F2-11"
FT /cell_type="hybridoma"
FT /tissue_type="spleen"
FT /db_xref="taxon:10090"
XX
SQ Sequence 366 BP; 100 A; 90 C; 85 G; 89 T; 2 other;
gagnnccagc tgcagcagtc tggacctgag ctggtaaagc ctggggcttc agtgaagatg 60
tcctgcaagg cttctggata cacattcact agctatgtta tgcactgggt gaatcagaag 120
cctgggcagg gccttgagtg gattggatat attaatcctt acaatgatgg tactaactac 180
aatgagaagt tcaaaggcaa ggccacactg acttcagaca aatcctccag cacagcctac 240
atggagttca gcagcctgac ctctgaggac tctgcggtct attactgtgc aagaaaaact 300
tcctactata gtaacctata ttactttgac tactggggcc aaggcaccac tctcacagtc 360
tcctca 366
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: l48662.fasta </h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>L48662 L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy chain mRNA.
aggtttttatattacaagcatactaagagactcgcgatgatcgcacaattccaaatgtgc
tcatgggtgtagcaagaacctcaaataaaagggcaaccatgagggtaaagtctccgcatg
agcccctgggacgcgagagactttctcccgctagtgggtcgaacctgcagtgtcgataat
tggagttaaaatcgcagcatttacggccatgaattgtgtcgatanacgattcacgcaatc
gttaagatcaggttcattgggntcacaaaccgtaggccccccgttgcctgacgcgtaacg
ttcggatttccgtgacttcatctgactactctgtcacattcttacacgacaagctcaaca
agccgg
>L48662 L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy chain mRNA.
gtggatggtatccctaacccatgacttgcgattccattgactaataccgatttcgctatg
cgaataatactgcacaataagcgctgggggttggtttaaanttgcgatgtattatcaggt
gcatcatacgcgtgtcttcaatcgcaggagaatacaaactcagtcccaagcctaaggcgc
gtgagacttcattagggcaacggatactgctaactagttaaactcgcatgtaacaactca
cctgagcggtcgtacatgggcctctcttcccgaagggttgttcgaaaaaagcattgatac
aggccaggcaagcaccacgtgtcagcactacgatggccgttntcaaagtagctcatacag
cctcgc
</pre>
</td></tr></table><p>
<p>
Each run will produce a different sequence.
<p>
Note that these two sequences have the same name.
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
This program may be useful for producing sets of sequences which
can be used to check the statistics of sequence similarity
finding software.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="msbar.html">msbar</a></td>
<td>Mutate sequence beyond all recognition</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Michael Schmitz (mschmitz © lbl.gov)
<br>
Lawrence Berkeley Labs, USA
<H2>
History
</H2>
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>
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