Bio::Tools::Run::PiseApplication::pftools.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::PiseApplication::pftools

SYNOPSIS

   #
 
 

DESCRIPTION

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)
 
 

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 (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/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.