NAME

Bio::Tools::Run::PiseApplication::pratt

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::pratt

      Bioperl class for:

        Pratt   pattern discovery (K. Sturzrehm, I. Jonassen)


      Parameters: 

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


                pratt (String)

                seq (Sequence)
                        Sequence File

                seqformat (Excl)
                        Sequence File format

                CM (Integer)
                        CM: min Nr of Seqs to Match (between 2 and 4)

                Cpct (Integer)
                        C%: min Percentage Seqs to Match

                PP (Excl)
                        PP: pos in seq

                PF (InFile)
                        PF: Restriction File name (if PP not off)

                PL (Integer)
                        PL: max Pattern Length

                PN (Integer)
                        PN: max Nr of Pattern Symbols

                PX (Integer)
                        PX: max Nr of consecutive x's

                FN (Integer)
                        FN: max Nr of flexible spacers

                FL (Integer)
                        FL: max Flexibility

                FP (Integer)
                        FP: max Flex.Product

                BI (Switch)
                        BI: Input Pattern Symbol File?

                BF (InFile)
                        BF: Input Pattern Symbol File name (if BI on)

                BN (Integer)
                        BN: Nr of Pattern Symbols Initial Search

                S (Excl)
                        S: Scoring

                treefile (InFile)
                        Tree File (if Scoring = tree)

                distfile (InFile)
                        Distances File (if Scoring = dist)

                swissprotdb (String)

                Z0 (Integer)
                        Z0

                Z1 (Integer)
                        Z1

                Z2 (Integer)
                        Z2

                Z3 (Integer)
                        Z3

                G (Excl)
                        G: Pattern Graph from:

                GF (InFile)
                        Alignment or Query Filename (if G set to al or query)

                E (Integer)
                        E: Search Greediness

                R (Switch)
                        R: Pattern Refinement

                RG (Switch)
                        RG: Generalise ambiguous symbols (if Pattern Refinement on)

                OF (OutFile)
                        OF: Output Filename

                OP (Switch)
                        OP: PROSITE Pattern Format

                ON (Integer)
                        ON: max number patterns

                OA (Integer)
                        OA: max number Alignments

                M (Switch)
                        M: Print Patterns in sequences

                MR (Integer)
                        MR: ratio for printing

                MV (Switch)
                        MV: print vertically

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/pratt.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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