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