NAME

Bio::Tools::Run::PiseApplication::dialign2

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::dialign2

      Bioperl class for:

        DIALIGN DNA and protein sequence alignment based on segment-to-segment comparison (Morgenstern, Dress, Werner)

        References:

                B. Morgenstern (1999). DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211 - 218.



      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/dialign2.html 
         for available values):


                dialign2 (String)

                sequence (Sequence)
                        Sequences
                        pipe: seqsfile

                protein_dna (Excl)
                        Nucleic acid or protein alignment

                threshold (Float)
                        Threshold

                translation (Switch)
                        Translation of nucleotide diagonals into peptide diagonals (DNA)

                max_simil (Integer)
                        Maximum number of * characters representing degree similarity

                fasta (Switch)
                        Alignment in fasta format

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/dialign2.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

 Title   : new()
 Usage   : my $dialign2 = Bio::Tools::Run::PiseApplication::dialign2->new($location, $email, @params);
 Function: Creates a Bio::Tools::Run::PiseApplication::dialign2 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 $dialign2 = $factory->program('dialign2');
 Example : -
 Returns : An instance of Bio::Tools::Run::PiseApplication::dialign2.