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Man Pages


Manual Reference Pages  -  RANDSEQ (1)

NAME

randseq - randomly shuffle a protein or DNA sequence

CONTENTS

Synopsis
Description
Examples
Options
Author

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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