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 listsReporting 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/issuesAUTHOR - 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