Bio::Tools::Run::PiseApplication::codonw.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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 (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.