BP_OLIGO_COUNT(1) User Contributed Perl Documentation BP_OLIGO_COUNT(1)NAME
bp_oligo_count - oligo count and frequency
SYNOPSIS
Usage: bp_oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
[-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
[-o/--out OUTFILE]
DESCRIPTION
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 EMBOSS.
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.
FEEDBACK
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.
bioperl-l@bioperl.org - 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:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Charles C. Kim
Email cckim@stanford.edu
HISTORY
Written July 2, 2001
Submitted to bioperl scripts project 2001/08/06
>> 100 x speed optimization by Heikki Lehvaslaiho
perl v5.20.2 2015-09-15 BP_OLIGO_COUNT(1)