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Shuffle randomizes the order of the symbols in a sequence without changing the composition.
Shuffle uses a random number generator to scramble the positions of the symbols in a sequence. The generator is initialized with the current time, so repeated shuffles should yield different results.
Here is a session using Shuffle to randomize the bases of gamma.seq:
% shuffle
SHUFFLE of what sequence ? gamma.seq
Begin (* 1 *) ?
End (* 11375 *) ?
Reverse (* No *) ?
What should I call the output file (* gamma.shuffle *) ?
%
The file gamma.shuffle now contains the shuffled contents of gamma.seq.
Shuffle accepts a single sequence as input. The function of Shuffle depends on whether your input sequence(s) are protein or nucleotide. Programs determine the type of a sequence by the presence of either Type: N or Type: P on the last line of the text heading just above the sequence. If your sequence(s) are not the correct type, see Appendix VI for information on how to change or set the type of a sequence.
Sample extracts sequence fragments randomly from sequence(s). You can set a sampling rate to determine how many fragments Sample extracts. Corrupt randomly introduces small numbers of substitutions, insertions, and deletions into nucleotide sequence(s).
All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
Minimal Syntax: % shuffle [-INfile=]gamma.seq -Default
Prompted Parameters:
-BEGin=1 -END=11375 sets the range of interest
-REVerse uses the reverse strand
[-OUTfile=]gamma.shuffle names the output file
Local Data Files: None
Optional Parameters:
-PREServe=2 preserves dinucleotide or dipeptide composition
in shuffled sequence
=3 preserves trinucleotide or tripeptide composition
in shuffled sequence
-NONUMbering suppresses the numbering in the output file
None.
You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
preserves the input sequence's dinucleotide or dipeptide composition in the output shuffled sequence. Use -PREServe=3 to preserve the trinucleotide or tripeptide composition.
suppresses the numbering in the output file.
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