DragonFly On-Line Manual Pages

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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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