SHUFFLE

Table of Contents

FUNCTION

DESCRIPTION

EXAMPLE

FUNCTION

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Shuffle randomizes the order of the symbols in a sequence without changing the composition.

DESCRIPTION

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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.

EXAMPLE

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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 *) ?

OUTPUT

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The file gamma.shuffle now contains the shuffled contents of gamma.seq.

INPUT FILES

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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 eitherType: 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, turn to Appendix VI for information on how to change or set the type of a sequence.

RELATED PROGRAMS

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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 or protein sequence(s).

COMMAND-LINE SUMMARY

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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.

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

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line.

-PREServe=2

Preserves the input sequence's dinucleotide or dipeptide composition in the output shuffled sequence. Use -PREServe=3 to preserve the trinucleotide or tripeptide composition.

-NONUMbering

Suppresses the numbering in the output file.

Printed: April 5, 2005 15:39

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