Bio::Tools::Run::PiseApplication::hmmscore(3)

NAME
Bio::Tools::Run::PiseApplication::hmmscore

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::hmmscore

      Bioperl class for:

        SAM     hmmscore - calculate NLL scores, smooth curves and Z-scores for sequences given a model (R. Hughey, A. Krogh)

        References:

                R. Hughey and A. Krogh., SAM: Sequence alignment and modeling software system. Technical Report UCSC-CRL-96-22, University of California, Santa Cruz, CA, September 1996.

      Parameters:

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

                hmmscore (String)

                run (String)
                        Run name

                db (Sequence)
                        Sequences to score against model (-db)

                model_file (InFile)
                        Model (-i)
                        pipe: sam_model

                id (String)
                        Sequence identifier(s) selection (separated by commas) (-id)

                nscoreseq (Integer)
                        Maximum number of sequences to be read (-nscoreseq)

                read_smooth (Switch)

                smooth_file (InFile)
                        Read a smooth curve from this smooth_file (-smooth_file and -read_smooth)

                adjust_score (Excl)
                        Adjust score option (-adjust_score)

                auto_fim (Switch)
                        Automatically add FIMs to the model before scoring when simple or complex null model subtraction is used (-auto_fim)

                jump_in_prob (Float)
                        Probability cost of jumping into the center of the model (if SW set) (-jump_in_prob)

                jump_out_prob (Float)
                        Probability cost of jumping out the center of the model (if SW set) (-jump_out_prob)

                SW (Excl)
                        Sequence scoring (-SW)

                window_size (Integer)
                        Window size for use in Z-score calculation (-window_size)

                Zmax (Float)
                        Z-score beyond which points are considered outliers during curve fitting (-Zmax)

                subtract_null (Excl)
                        Null model scoring (-subtract_null)

                select_score (Excl)
                        Selection criteria used for listing sequence scores in file runname.dist (-select_score)

                select_seq (Excl)
                        Selection criteria used for placing sequences in the file runname.sel (-select_seq)

                NLLNull (Float)
                        If select_score/seq=1, sequences with an NLL or NLLNull score smaller than this number are selected (-NLLNull)

                NLLperBase (Float)
                        If select_score/seq=2, sequences with an NLL score per base smaller than this number are selected (-NLLperBase)

                NLLperNode (Float)
                        If select_score/seq=3, sequences with an NLL score per model node smaller than this number are selected (-NLLperNode)

                NLLFile (InFile)
                        File with already-calculated sequence distances (-NLLFile)

                calc_smooth (Switch)
                        Calculate a smooth curve and write it to smooth_file (-calc_smooth)

                sort (Excl)
                        Sequence sorting (-sort)

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/hmmscore.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

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