Bio::Tools::Run::PiseApplication::wise2(3)

NAME
Bio::Tools::Run::PiseApplication::wise2

SYNOPSIS
  #

DESCRIPTION
Bio::Tools::Run::PiseApplication::wise2

      Bioperl class for:

        WISE2   comparisons of protein/DNA sequences (E. Birney)

      Parameters:

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/wise2.html
         for available values):

                wise2 (Excl)
                        Wise program

                protein (Sequence)
                        Protein sequence File (if no HMM, see help)

                dna (Sequence)
                        DNA sequence File

                quiet (String)

                dna_start (Integer)
                        Start position in dna (-u)

                dna_end (Integer)
                        End position in dna (-v)

                strand (Excl)
                        Strand comparison

                tabs (Switch)
                        Report positions as absolute to truncated/reverse sequence (-tabs)

                protein_start (Integer)
                        Start position in protein (-s)

                protein_end (Integer)
                        End position in protein (-t)

                gap (Integer)
                        Gap penalty (-g)

                ext (Integer)
                        Gap extension penalty (-e)

                hmmer (InFile)
                        HMMer file (instead of protein) (-hmmer)
                        pipe: hmmfile

                hname (String)
                        Name of HMM rather than using the filename (-hname)

                init (Excl)
                        Type of match (-init)

                subs (Float)
                        Substitution error rate (-subs)

                indel (Float)
                        Insertion/deletion error rate (-indel)

                cfreq (Excl)
                        Using codon bias or not (-cfreq)

                splice (Excl)
                        Using splice model or GT/AG (-splice)

                intron (Excl)
                        Use tied model for introns (-intron)

                null (Excl)
                        Random Model as synchronous or flat (-null)

                alln (Float)
                        Probability of matching a NNN codon (-alln)

                insert (Excl)
                        Protein insert model (-insert)

                pretty (Switch)
                        Show pretty ascii output (-pretty)

                pseudo (Switch)
                        Mark genes with frameshifts as pseudogenes (-pseudo)

                genes (Switch)
                        Show gene structure (-genes)

                embl (Switch)
                        show EMBL feature format with CDS key (-embl)

                diana (Switch)
                        show EMBL feature format with misc_feature key for diana (-diana)

                para (Switch)
                        Show parameters (-para)

                sum (Switch)
                        Show summary output (-sum)

                cdna (Switch)
                        Show cDNA (-cdna)

                trans (Switch)
                        Show protein translation (-trans)

                ace (Switch)
                        Ace file gene structure (-ace)

                gff (Switch)
                        Gene Feature Format file (-gff)

                gener (Switch)
                        Raw gene structure (-gener)

                alb (Switch)
                        Show logical AlnBlock alignment (-alb)

                pal (Switch)
                        Show raw matrix alignment (-pal)

                block (Integer)
                        Length of main block in pretty output (-block)

                divide (String)
                        divide string for multiple outputs (-divide)

                erroroffstd (Switch)
                        No warning messages (-erroroffstd)

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/wise2.html

•   Bio::Tools::Run::PiseApplication

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

•   Bio::Tools::Run::PiseJob

  new
 Title   : new()
 Usage   : my $wise2 = Bio::Tools::Run::PiseApplication::wise2->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::wise2 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 $wise2 = $factory->program('wise2');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::wise2.