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.\" ========================================================================
.\"
.IX Title "BP_OLIGO_COUNT 1p"
.TH BP_OLIGO_COUNT 1p "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
bp_oligo_count \- oligo count and frequency
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  Usage:  bp_oligo_count [\-h/\-\-help] [\-l/\-\-length OLIGOLENGTH]
\&          [\-f/\-\-format SEQFORMAT] [\-i/\-\-in/\-s/\-\-sequence SEQFILE]
\&          [\-o/\-\-out OUTFILE]
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This scripts counts occurrence and frequency for all oligonucleotides
of given length.
.PP
It can be used to determine what primers are useful for
frequent priming of nucleic acid for random labeling.
.PP
Note that this script could be run by utilizing the compseq
program which is part of \s-1EMBOSS.\s0
.SH "OPTIONS"
.IX Header "OPTIONS"
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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Charles C. Kim"
.IX Header "AUTHOR - Charles C. Kim"
Email cckim@stanford.edu
.SH "HISTORY"
.IX Header "HISTORY"
Written July 2, 2001
.PP
Submitted to bioperl scripts project 2001/08/06
.PP
>> 100 x speed optimization by Heikki Lehvaslaiho