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 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  fre-
	      quencies 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 bet-
	      ter  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 align-
	      ment 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  dif-
	      ferent 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

Biosquid 1.9g							   January 2003 							shuffle(1)