NAME

Bio::Tools::Run::PiseApplication::est2genome

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::est2genome

      Bioperl class for:

        EST2GENOME      Align EST and genomic DNA sequences (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/est2genome.html 
         for available values):


                est2genome (String)

                init (String)

                est (Sequence)
                        EST sequence(s) (-est)
                        pipe: seqsfile

                genome (Sequence)
                        Genomic sequence (-genome)
                        pipe: seqfile

                match (Integer)
                        Score for matching two bases (-match)

                mismatch (Integer)
                        Cost for mismatching two bases (-mismatch)

                gappenalty (Integer)
                        Gap penalty (-gappenalty)

                intronpenalty (Integer)
                        Intron penalty (-intronpenalty)

                splicepenalty (Integer)
                        Splice site penalty (-splicepenalty)

                minscore (Integer)
                        Minimum accepted score (-minscore)

                reverse (Switch)
                        Reverse orientation (-reverse)

                splice (Switch)
                        Use donor and acceptor splice sites (-splice)

                mode (String)
                        Comparison mode (-mode)

                best (Switch)
                        Print out only best alignment (-best)

                space (Float)
                        Space threshold (in megabytes) (-space)

                shuffle (Integer)
                        Shuffle (-shuffle)

                seed (Integer)
                        Random number seed (-seed)

                outfile (OutFile)
                        outfile (-outfile)

                align (Switch)
                        Show the alignment (-align)

                width (Integer)
                        Alignment width (-width)

                auto (String)

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/est2genome.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $est2genome = Bio::Tools::Run::PiseApplication::est2genome->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::est2genome 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 $est2genome = $factory->program('est2genome');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::est2genome.