NAME

Bio::Tools::Run::PiseApplication::prophecy

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::prophecy

      Bioperl class for:

	PROPHECY	Creates matrices/profiles from multiple alignments (EMBOSS)


      Parameters: 

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


		prophecy (String)

		init (String)

		sequence (Sequence)
			sequence -- gapany [set of sequences] (-sequence)
			pipe: seqsfile

		type (Excl)
			Select type -- Profile type (-type)

		name (String)
			Enter a name for the profile (-name)

		threshold (Integer)
			Enter threshold reporting percentage (-threshold)

		datafile (Excl)
			Scoring matrix (-datafile)

		open (Float)
			Gap opening penalty (-open)

		extension (Float)
			Gap extension penalty (-extension)

		outf (OutFile)
			outf (-outf)

		auto (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/MailList.shtml  - 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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

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/prophecy.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $prophecy = Bio::Tools::Run::PiseApplication::prophecy->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::prophecy 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 $prophecy = $factory->program('prophecy');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::prophecy.