This is the command shuffle that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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