RSS(1) General Commands Manual RSS(1) 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 al- gorithm 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 local RSS(1)
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