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bp_oligo_countp - Online in the Cloud

Run bp_oligo_countp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bp_oligo_countp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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.

[email protected] - 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 [email protected]

HISTORY


Written July 2, 2001

Submitted to bioperl scripts project 2001/08/06

>> 100 x speed optimization by Heikki Lehvaslaiho

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