1BP_OLIGO_COUNT(1) User Contributed Perl Documentation BP_OLIGO_COUNT(1)
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6 oligo_count - oligo count and frequency
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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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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
18 priming 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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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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29 Mailing Lists
30 User feedback is an integral part of the evolution of this and other
31 Bioperl modules. Send your comments and suggestions preferably to the
32 Bioperl mailing list. Your participation is much appreciated.
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34 bioperl-l@bioperl.org - General discussion
35 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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37 Reporting Bugs
38 Report bugs to the Bioperl bug tracking system to help us keep track of
39 the bugs and their resolution. Bug reports can be submitted via the
40 web:
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42 http://bugzilla.open-bio.org/
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45 Email cckim@stanford.edu
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48 Written July 2, 2001
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50 Submitted to bioperl scripts project 2001/08/06
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52 >> 100 x speed optimization by Heikki Lehvaslaiho
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56perl v5.12.0 2010-04-29 BP_OLIGO_COUNT(1)