BP_OLIGO_COUNT(1p) User Contributed Perl Documentation BP_OLIGO_COUNT(1p)NAME
oligo_count - oligo count and frequency
SYNOPSIS
Usage: 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://redmine.open-bio.org/projects/bioperl/
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 v5.14.2 2012-03-02 BP_OLIGO_COUNT(1p)
Check Out this Related Man Page
Bio::Coordinate::Result::Gap(3pm) User Contributed Perl Documentation Bio::Coordinate::Result::Gap(3pm)NAME
Bio::Coordinate::Result::Gap - Another name for Bio::Location::Simple
SYNOPSIS
$loc = Bio::Coordinate::Result::Gap->new(-start=>10,
-end=>30,
-strand=>1);
DESCRIPTION
This is a location object for coordinate mapping results.
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 one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki Lehvaslaiho
Email heikki-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
perl v5.14.2 2012-03-02 Bio::Coordinate::Result::Gap(3pm)
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