NAME

Bio::Tools::Run::PiseApplication::saps

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::saps

      Bioperl class for:

        SAPS    Statistical Analysis of Protein Sequences (V. Brendel)

        References:

                Brendel, V., Bucher, P., Nourbakhsh, I., Blaisdell, B.E., Karlin, S. (1992) Methods and algorithms for statistical analysis of protein sequences. Proc. Natl. Acad. Sci. USA 89: 2002-2006. 



      Parameters: 

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


                saps (String)

                seq (Sequence)
                        Protein sequence(s) File
                        pipe: seqfile

                documented (Switch)
                        Generate documented output (-d)

                terse (Switch)
                        Generate terse output (-t)

                verbose (Switch)
                        Generate verbose output (-v)

                table (Switch)
                        Append computer-readable table summary output (-T)

                specie (Excl)
                        Use this specie for quantile comparisons (-s)

                H_positive (Switch)
                        Count H as positive charge (-H)

                analyze (String)
                        Analyze spacings of amino acids X, Y, .... (-a)

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/saps.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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