67 lines
3.3 KiB
Plaintext
67 lines
3.3 KiB
Plaintext
shuffle.doc update 3 Feb 94
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SYNOPSIS
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shuffle -sn [-wn -on]
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DESCRIPTION
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Shuffles sequences locally. See Lipman DJ, Wilbur WJ, Smith TF
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and Waterman MS (1984) On the statistical significance of nucleic
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acid similarities. Nucl. Acids Res. 12:215-226.
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-sn n is a random integer between 0 and 32767. This number
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must be provided for each run.
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-wn n is an integer, indicating the width of the window for
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random localization. If w exceeds the length of a sequence,
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or is negative, the entire sequence is scrambled as a single
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window. This is also the case if w is not specified.
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-on n is an integer, indicating the number of nucleotides
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overlap between adjacent windows. It should never exceed
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the window size. o defaults to 0 if not specified.
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If w and o are specified, overlapping windows of w nucleotides
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are shuffled, thus preserving the local characteristic base
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composition. Windows overlap by o nucleotides.
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If w and o are not specified, each sequence is shuffled globally,
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thus preserving the overall base composition, but not the local
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variations in comp.
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Any number of sequences may be processed from a single input
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file. In Pearson-format files, each new sequence begins with a
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'>' comment line, indicating the name and a short description of
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the sequence.
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No distinction is made between protein or nucleic acid sequences.
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That is, shuffle will read any of the following characters as
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sequence:
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T,U,C,A,G,N,R,Y,M,W,S,K,D,H,V,B,L,Z,F,P,E,I,Q,X,*,-
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where '*' is the result of translating a stop codon, and '-'
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is a gap generated during sequence alignment. Lowercase is
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also accepted.
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EXAMPLE
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A sample output file is shown below. Note that the first two
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lines of output are comment lines, listing the version of the
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program and the parameters used in the run.
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>SHUFFLE VERSION 11/ 8/93
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>RANDOM SEED: 9873 WINDOW: 12 OVERLAP: 3
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>BAZFAZ - Borborigmus azerbi F-actin-zeta gene
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ctgagtagctagtcctaaatagttagtccatagtactagtacgggtcgtt
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cacccttgggcagtg.....(etc.)
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AUTHOR
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Dr. Brian Fristensky
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Dept. of Plant Science
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University of Manitoba
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Winnipeg, MB Canada R3T 2N2
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Phone: 204-474-6085
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FAX: 204-261-5732
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frist@cc.umanitoba.ca
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REFERENCE
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Fristensky, B. (1993) Feature expressions: creating and manipulating
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sequence datasets. Nucleic Acids Research 21:5997-6003.
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