NAME

Bio::Tools::Run::PiseApplication::hmmbuild

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::hmmbuild

      Bioperl class for:

        HMMER   hmmbuild - construct an HMM from a multiple sequence alignment (S. Eddy)


      Parameters: 

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


                hmmbuild (String)

                alignfile (Sequence)
                        Aligned sequences File
                        pipe: hmmer_alig

                hmmfile (OutFile)

                multiple_local (Switch)
                        multiple local alignments (-f)

                single_global (Switch)
                         single global alignment (-g)

                single_local (Switch)
                        single local alignment (-s)

                name (String)
                        name the HMM (-n 'name')

                re_save (OutFile)
                        Re-save the starting alignment to 'file', in SELEX format. (-o 'file')

                append (InFile)
                        append the model to an existing HMMs file (-A)

                amino (Switch)
                        Force the sequence alignment to be interpreted as amino acid sequences. (--amino)

                archpri (Float)
                        Set the 'architecture prior' to x (--archpri x)

                binary (Switch)
                        Write the HMM to hmmfile in HMMER binary format instead of readable ASCII text. (--binary)

                cfile (Switch)
                        Save the observed emission and transition counts to a file (--cfile f)

                fast (Switch)
                        Quickly and heuristically determine the architecture of the model (--fast)

                gapmax (Float)
                        Controls the --fast model construction algorithm, (--gapmax x)

                hand (Switch)
                        Specify the architecture of the model by hand (--hand)

                idlevel (Float)
                         (--idlevel x)

                noeff (Switch)
                        Turn off the effective sequence number calculation (--noeff)

                nucleic (Switch)
                        Force the alignment to be interpreted as nucleic acid sequence (--nucleic)

                null (InFile)
                        null model (--null f)

                pam (InFile)
                        heuristic PAM based prior (--pam f)

                pamwgt (Float)
                        Controls the weight on a PAM-based prior. (--pamwgt x)

                pbswitch (Integer)
                        PB weights (--pbswitch n)

                prior (InFile)
                        Dirichlet prior (--prior f)

                swentry (Float)
                        Controls the total probability that is distributed to local entries into the model (--swentry x)

                swexit (Float)
                        Controls the total probability that is distributed to local exits from the model (--swexit x)

                verbose (Switch)
                        Print more possibly useful stuff, such as the individual scores for each sequence in the alignment. (--verbose)

                wblosum (Switch)
                        Use the BLOSUM filtering algorithm to weight the sequences (--wblosum)

                wgsc (Switch)
                        Use the Gerstein/Sonnhammer/Chothia ad hoc sequence weighting algorithm. (--wgsc)

                wme (Switch)
                        Use the Krogh/Mitchison maximum entropy algorithm to 'weight' the sequences. (--wme)

                wnone (Switch)
                        Turn off all sequence weighting. (--wnone)

                wpb (Switch)
                        Use the Henikoff position-based weighting scheme (--wpb)

                wvoronoi (Switch)
                        Use the Sibbald/Argos Voronoi sequence weighting algorithm in place of the default GSC weighting. (--wvoronoi)

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/hmmbuild.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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