shuffle [options] seqfile
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.
- -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.
- --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.
afetch(1), alistat(1), compalign(1),
compstruct(1), revcomp(1), seqsplit(1),
seqstat(1), sfetch(1), sindex(1), sreformat(1),
stranslate(1), weight(1).
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