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NAME
       randseq - randomly shuffle a protein or DNA sequence

SYNOPSIS
       randseq [ -w # -O file ] sequence-file-1

       randseq [-w # -O] - interactive mode

DESCRIPTION
       randseq	produces  a  shuffled amino acid or DNA sequence with the same
       length and composition as the input sequence.  randseq  uses  the  same
       shuffling  algorithm  as prss and prdf.	Shuffled sequences can be used
       to evaluate the accuracy	 of  the  statistical  estimates  produced  by
       BLAST,  FASTA,  or  SSEARCH.   Searches	done  with a randomly shuffled
       sequence should have an expectation value around 1.0 (BLASTP p-value  =
       0.63).

EXAMPLES
       randseq
	       -w 20 mgstm1.aa > mgstm1.raa

       Shuffle	the  sequence in "mgstm1.aa" using a local window of length 20
       and send the output to "mgstm1.raa".

OPTIONS
       -w #   use local window for shuffle with window size #.

       -O file
	      send output to file.

AUTHOR
       Bill Pearson
       wrp@virginia.EDU

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