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 composition 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
composition. 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 composition); generate output sequence using the
same 0th order Markov frequencies.
-1 Calculate 1st order Markov frequencies for each input sequence
(e.g. diresidue composition); 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 composition 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 varying 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 format. 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.
SEE ALSO
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 School of Medicine Freely distributed under
the GNU General Public License (GPL) See COPYING 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: eddy@genetics.wustl.edu