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

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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.bioperl.org/ Catherine Letondal (letondal@pasteur.fr) 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. This software is provided "as is" without warranty of any kind. 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.