NAME

Bio::Tools::Run::PiseApplication::water

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::water

      Bioperl class for:

	WATER	Smith-Waterman local alignment. (EMBOSS)


      Parameters: 

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


		water (String)

		init (String)

		sequencea (Sequence)
			sequencea -- any [single sequence] (-sequencea)
			pipe: seqfile

		seqall (Sequence)
			seqall [sequences] (-seqall)
			pipe: seqsfile

		gapopen (Float)
			Gap opening penalty (-gapopen)

		gapextend (Float)
			Gap extension penalty (-gapextend)

		datafile (Excl)
			Matrix file (-datafile)

		brief (Switch)
			Brief identity and similarity (-brief)

		outfile (OutFile)
			outfile (-outfile)
			pipe: readseq_ok_alig

		outfile_aformat (Excl)
			Alignment output format (-aformat)

		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/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/water.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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