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.