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

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.