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/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/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.