NAME

Bio::Tools::Run::PiseApplication::primo

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::primo

      Bioperl class for:

	PRIMO	A primer design tool (Kupfer, Li)

	References:

		P. Li, K. C. Kupfer, C. J. Davies, D. Burbee, G. A. Evans, and H. R. Garner. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40:476-485 (1997).



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/primo.html 
         for available values):


		primo (String)

		input_file_name (InFile)
			Sequence data

		all (String)

		cover (Switch)
			cover template with walking-primers on both strands (-cover)

		print (Switch)
			print formatted/annotated sequence to log file (-print)

		regions_file (InFile)
			Regions file (-read)

		qual_file (InFile)
			Quality datafile file

		repeats_file (InFile)
			Repeats file

		oligo_file (InFile)
			Oligo file

		rf (String)

		qf (String)

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:

http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• http://bioweb.pasteur.fr/seqanal/interfaces/primo.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $primo = Bio::Tools::Run::PiseApplication::primo->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::primo object.
          This method should not be used directly, but rather by 
          a Bio::Tools::Run::AnalysisFactory::Pise instance.
          my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
          my $primo = $factory->program('primo');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::primo.