NAME

Bio::Tools::Run::PiseApplication::codonw

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::codonw

      Bioperl class for:

	codonw	Correspondence Analysis of Codon Usage (J. Peden)


      Parameters: 

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


		codonw (String)

		outfiles (String)

		seqfile (Sequence)
			Sequences File

		gc (Excl)
			Genetic codes

		fop_values (Excl)
			Fop/CBI values

		cai_values (Excl)
			CAI values

		output_type (Switch)
			Output Computer readable

		genes (Switch)
			Concatenate genes (instead of individual genes)

		CAI (Switch)
			Codon Adaptation Index (CAI)

		Fop (Switch)
			Frequency of OPtimal codons (Fop)

		CBI (Switch)
			Codon bias index (CBI)

		cai_file (InFile)
			User input file of CAI values (may be computed by a previous COA)
			pipe: codonw_coa_file

		fop_file (InFile)
			User input file of Fop values (may be computed by a previous COA)

		cbi_file (InFile)
			User input file of CBI values (may be computed by a previous COA)

		ENc (Switch)
			Effective Number of Codons (ENc)

		GC (Switch)
			GC content of gene (G+C)

		GC3s (Switch)
			GC of silent 3rd codon posit. (GC3s)

		silent_bc (Switch)
			Silent base composition

		all_indices (Switch)
			All the above indices

		L_sym (Integer)
			Number of synonymous codons (L_sym)

		L_aa (Switch)
			Total Number of synonymous and non-synonymous codons (L_aa)

		Hydro (Switch)
			Hydrophobicity of protein (Hydro)

		Aromo (Switch)
			Aromaticity of protein (Aromo)

		bulk_output_option (Excl)
			Other output option

		coa_cu (Switch)
			COA on codon usage

		coa_rscu (Switch)
			COA on RSCU

		coa_aa (Switch)
			COA on Amino Acid usage

		coa_expert (Switch)
			Generate detailed(expert) statistics on COA

		coa_axes (Integer)
			Select number of axis to record

		coa_num (Integer)
			Select number of genes to use to identify optimal codons

		cai_coa (OutFile)
			pipe: codonw_coa_file

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/codonw.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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