SIMPLE SOLUTIONS

# SHUFFLE(1) - man page online | user commands

Randomize the sequences in a sequence file.

Chapter
January 2003
```shuffle(1)                               Biosquid Manual                               shuffle(1)

NAME
shuffle - randomize the sequences in a sequence file

SYNOPSIS
shuffle [options] seqfile

DESCRIPTION
shuffle reads a sequence file seqfile, randomizes each sequence, and prints the randomized
sequences in FASTA format on standard output. The sequence names are unchanged; this
allows you to track down the source of each randomized sequence if necessary.

The default is to simply shuffle each input sequence, preserving monosymbol composition
exactly. To shuffle each sequence while preserving both its monosymbol and disymbol compo‐
sition exactly, use the -d option.

The -0 and -1 options allow you to generate sequences with the same Markov properties as
each input sequence. With -0, for each input sequence, 0th order Markov statistics are
collected (e.g. symbol composition), and a new sequence is generated with the same compo‐
sition.  With -1, the generated sequence has the same 1st order Markov properties as the
input sequence (e.g.  the same disymbol frequencies).

Note that the default and -0, or -d and -1, are similar; the shuffling algorithms preserve
composition exactly, while the Markov algorithms only expect to generate a sequence of
similar composition on average.

Other shuffling algorithms are also available, as documented below in the options.

OPTIONS
-0     Calculate 0th order Markov frequencies of each input sequence (e.g. residue compo‐
sition); generate output sequence using the same 0th order Markov frequencies.

-1     Calculate 1st order Markov frequencies for each input sequence (e.g. diresidue com‐
position); generate output sequence using the same 1st order Markov frequencies.
The first residue of the output sequence is always the same as the first residue of
the input sequence.

-d     Shuffle the input sequence while preserving both monosymbol and disymbol composi‐
tion exactly. Uses an algorithm published by  S.F. Altschul and B.W. Erickson, Mol.
Biol. Evol. 2:526-538, 1985.

-h     Print brief help; includes version number and summary of all options, including
expert options.

-l     Look only at the length of each input sequence; generate an i.i.d. output protein
sequence of that length, using monoresidue frequencies typical of proteins (taken
from Swissprot 35).

-n <n> Make <n> different randomizations of each input sequence in seqfile, rather than
the default of one.

-r     Generate the output sequence by reversing the input sequence. (Therefore only one
"randomization" per input sequence is possible, so it's not worth using -n if you
use reversal.)

-t <n> Truncate each input sequence to a fixed length of exactly <n> residues. If the
input sequence is shorter than <n> it is discarded (therefore the output file may
contain fewer sequences than the input file).  If the input sequence is longer than
<n> a contiguous subsequence is randomly chosen.

-w <n> Regionally shuffle each input sequence in window sizes of <n>, preserving local
residue composition in each window.  Probably a better shuffling algorithm for
biosequences with nonstationary residue composition (e.g. composition that is vary‐
ing along the sequence, such as between different isochores in human genome
sequence).

-B     (Babelfish). Autodetect and read a sequence file format other than the default
(FASTA). Almost any common sequence file format is recognized (including Genbank,
EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, and Stockholm, GCG MSF,
and Clustal alignment formats). See the printed documentation for a complete list
of supported formats.

EXPERT OPTIONS
--informat <s>
Specify that the sequence file is in format <s>, rather than the default FASTA for‐
mat.  Common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or
PHYLIP; see the printed documentation for a complete list of accepted format names.
This option overrides the default expected format (FASTA) and the -B Babelfish
autodetection option.

--nodesc
Do not output any sequence description in the output file, only the sequence names.

--seed <s>
Set the random number seed to <s>.  If you want reproducible results, use the same
seed each time.  By default, shuffle uses a different seed each time, so does not
generate the same output in subsequent runs with the same input.

afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1),
sfetch(1), sindex(1), sreformat(1), stranslate(1), weight(1).

AUTHOR
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University
ING in the source code distribution for more details, or contact me.

Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX  : 1-314-362-2157
Email: @genetics.wustl.edu

Biosquid 1.9g                              January 2003                                shuffle(1)```
 This manual Reference Other manuals shuffle(1) referred by afetch(1) | alistat(1) | compalign(1) | revcomp(1) | seqsplit(1) | seqstat(1) | sfetch(1) | sindex(1) | sreformat(1) | stranslate(1) | weight(1) refer to afetch(1) | alistat(1) | compalign(1) | compstruct(1) | revcomp(1) | seqsplit(1) | seqstat(1) | sfetch(1) | sindex(1) | sreformat(1) | stranslate(1) | weight(1)