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bp_oligo_count - oligo count and frequency


Usage: bp_oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
[-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
[-o/--out OUTFILE]


This scripts counts occurrence and frequency for all oligonucleotides of given length.

It can be used to determine what primers are useful for frequent priming of nucleic acid
for random labeling.

Note that this script could be run by utilizing the compseq program which is part of


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


Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to the Bioperl mailing list. Your participation
is much appreciated.

[email protected] - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
resolution. Bug reports can be submitted via the web:


AUTHOR - Charles C. Kim

Email [email protected]


Written July 2, 2001

Submitted to bioperl scripts project 2001/08/06

>> 100 x speed optimization by Heikki Lehvaslaiho

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