NAME

Bio::Tools::Run::PiseApplication::showalign

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::showalign

      Bioperl class for:

	SHOWALIGN	Displays a multiple sequence alignment (EMBOSS)


      Parameters: 

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


		showalign (String)

		init (String)

		sequence (Sequence)
			sequence -- gapany [set of sequences] (-sequence)
			pipe: seqsfile

		refseq (String)
			The number or the name of the reference sequence (-refseq)

		bottom (Switch)
			Display the reference sequence at the bottom (-bottom)

		show (Excl)
			What to show -- What to show (-show)

		order (Excl)
			Output order of the sequences -- Output order of the sequences (-order)

		similarcase (Switch)
			Show similar residues in lower-case (-similarcase)

		matrix (Excl)
			Similarity scoring Matrix file (-matrix)

		uppercase (Integer)
			Regions to put in uppercase (eg: 4-57,78-94) (-uppercase)

		number (Switch)
			Number the sequences (-number)

		ruler (Switch)
			Display ruler (-ruler)

		width (Integer)
			Width of sequence to display (-width)

		margin (Integer)
			Length of margin for sequence names (-margin)

		html (Switch)
			Use HTML formatting (-html)

		highlight (Integer)
			Regions to colour in HTML (eg: 4-57 red 78-94 green) (-highlight)

		plurality (Float)
			Plurality check % for consensus (-plurality)

		setcase (Float)
			Threshold above which the consensus is given in uppercase (-setcase)

		identity (Float)
			Required % of identities at a position fro consensus (-identity)

		consensus (Switch)
			Display the consensus line (-consensus)

		outfile (OutFile)
			Output sequence details to a file (-outfile)

		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/showalign.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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