1BP_OLIGO_COUNT(1)     User Contributed Perl Documentation    BP_OLIGO_COUNT(1)
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NAME

6       oligo_count - oligo count and frequency
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SYNOPSIS

9         Usage:  oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
10                 [-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
11                 [-o/--out OUTFILE]
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DESCRIPTION

14       This scripts counts occurrence and frequency for all oligonucleotides
15       of given length.
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17       It can be used to determine what primers are useful for frequent prim‐
18       ing of nucleic acid for random labeling.
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20       Note that this script could be run by utilizing the compseq program
21       which is part of EMBOSS.
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OPTIONS

24       The default sequence format is fasta. If no outfile is given, the
25       results will be printed to standard out. All other options can entered
26       interactively.
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FEEDBACK

29       Mailing Lists
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31       User feedback is an integral part of the evolution of this and other
32       Bioperl modules. Send your comments and suggestions preferably to the
33       Bioperl mailing list.  Your participation is much appreciated.
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35         bioperl-l@bioperl.org                  - General discussion
36         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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38       Reporting Bugs
39
40       Report bugs to the Bioperl bug tracking system to help us keep track of
41       the bugs and their resolution. Bug reports can be submitted via the
42       web:
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44         http://bugzilla.open-bio.org/
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AUTHOR - Charles C. Kim

47       Email cckim@stanford.edu
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HISTORY

50       Written July 2, 2001
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52       Submitted to bioperl scripts project 2001/08/06
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54       >> 100 x speed optimization by Heikki Lehvaslaiho
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58perl v5.8.8                       2007-05-07                 BP_OLIGO_COUNT(1)