NAME

Bio::Tools::Run::PiseApplication::hmmpfam

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::hmmpfam

      Bioperl class for:

        HMMER   hmmpfam - search sequences against an HMM database (S. Eddy)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/hmmpfam.html 
         for available values):


                hmmpfam (String)

                toto (String)

                seqfile (Sequence)
                        Sequence file
                        pipe: seqfile

                HMMDB (Excl)
                        HMM database

                nucleic_acid (Switch)
                        Force nucleic acid models and sequences (-n)

                n_best (Integer)
                        number of reported alignments (-A n)

                E_value_cutoff (Float)
                        E_value cutoff (-E x)

                Bit_cutoff (Float)
                        Bit score cutoff (-T x)

                E_value_calculation (Integer)
                        Control of E_value calculation (-Z n)

                acc (Switch)
                        Report accessions instead of names in the output reports (--acc)

                compat (Switch)
                        Use the output format of HMMER 2.1.1 (--compat)

                domE (Float)
                        E-value cutoff for the per-domain ranked hit list (--domE x)

                domT (Float)
                        bit score cutoff for the per-domain ranked hit list (--domT x)

                forward (Switch)
                        forward algorithm (--forward)

                null2 (Switch)
                        turns off the second post processing step (--null2)

                xnu (Switch)
                        turns on XNU filtering (--xnu)

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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

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/hmmpfam.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

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