++ed by:
FIBO CJFIELDS GENEHACK THALJEF MAJENSEN

6 PAUSE users
6 non-PAUSE users.

Christopher Fields
and 1 contributors

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