Bio::Tools::Run::PiseApplication::pftools # Bio::Tools::Run::PiseApplication::pftools Bioperl class for: PFTOOLS Profile Tools (P. Bucher) References: Bucher P, Karplus K, Moeri N and Hofmann, K. (1996). A flexible motif search technique based on generalized profiles. Comput. Chem. 20:3-24. Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/pftools.html for available values): pftools (Excl) PFTOOLS program clean_output (String) fastaformat (Switch) seqfile (Sequence) Sequence File prosite (Switch) Scan PROSITE db (default)? profiledb (InFile) Profile db (PROSITE/NUCSITE format) (if not PROSITE) pfscan_cutoff (Integer) Cut-off value profile (InFile) Profile File (PROSITE/NUCSITE format, or see next option) pipe: gcg_profile gcg2psa (Switch) Convert the profile from GCG format to PROSITE format ? aa_or_nuc_db (Excl) protein or nucleotid db aadb (Excl) Protein Database nucdb (Excl) Nucleotid Database pfsearch_cutoff (Integer) Cut-off value psa2msa (Switch) reformat PSA result file to Fasta multiple sequence alignment file? stdinput (Switch) compl (Switch) Search the complementary strands of DNA sequences as well (-b) raw_score (Switch) Use raw scores rather than normalized scores for match selection. Normalized scores will not be listed in the output. (-r) unique (Switch) Forces DISJOINT=UNIQUE (-u) optimal (Switch) Report optimal alignment scores for all sequences regardless of the cut-off value (-a)? listseq (Switch) List the sequences of the matched regions as well. The output will be a Pearson/Fasta-formatted sequence library. (-s) psa_format (Switch) List profile-sequence alignments in pftools PSA format. (-x) between (Switch) Display alignments between the profile and the matched sequence regions in a human-friendly format. (-y)

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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/pftools.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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