RSS(1)RSS(1)NAMErandseq - randomly shuffle a protein or DNA sequence
SYNOPSISrandseq [ -w # -O file ] sequence-file-1
randseq [-w # -O] - interactive mode
DESCRIPTIONrandseq 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).
EXAMPLESrandseq-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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