[Bioperl-l] Shuffling sequences

[Morten Lindow]

I use shuffle from The HMMER package by Sean Eddy. Has a lot of nice 
options to preserve dinucleotide content and other stuff. See below.

Morten

shuffle -h
shuffle - generated shuffled (or otherwise randomized) sequence
HMMER 2.2g (August 2001)
Copyright (C) 1992-2001 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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Usage: shuffle [-options] <seqfile>
  Available options:
  -h         : help; print version and usage info
  -n <n>     : make <n> samples per input seq (default 1)
  -t <n>     : truncate/delete inputs to fixed length <n>

  Default: shuffle each input randomly, preserving mono-symbol composition.
  Other choices (exclusive; can't use more than one) :
  -d         : shuffle but preserve both mono- and di-symbol composition
  -0         : generate with same 0th order Markov properties as each input
  -1         : generate with same 1st order Markov properties as each input
  -l         : make iid sequences of same number and length as inputs
  -r         : reverse inputs
  -w <n>     : regionally shuffle inputs in window size <n>
  -i         : make [-n] iid seqs of length [-t] of type [--dna|--amino];
               when -i is set, no <seqfile> argument is used

  --alignment    : <seqfile> is an alignment; shuffle the columns
  --amino        : synthesize protein sequences [default] (see -i, -l)
  --dna          : synthesize DNA sequences (see -i, -l))
  --informat <s> : specify sequence file format <s>
  --nodesc       : remove sequence description lines
  --seed <s>     : set random number seed to <s>













KHOUEIRY pierre wrote:

> Hi all,
> I'm searching for the bioperl Method that shuffle/randomize  a given 
> protein sequence. I need to shuffle my fasta sequence 1000 times to 
> make a statistics test on.
> thanks in advance
>
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