Bio::Tools::Run::PiseApplication::tacg.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::tacg

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::tacg
       Bioperl class for:
 
         TACG    Restriction Enzyme analysis (Mangalam)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/tacg.html 
          for available values):
 
 
                 tacg (String)
 
                 sequence (Sequence)
                         DNA Sequence (raw sequence)
 
                 beginning (Integer)
                         Beginning of a subsequence in your sequence (-b)
 
                 end (Integer)
                         End of a subsequence in your sequence (-e)
 
                 topology (Excl)
                         Form (or topology) of DNA (-f)
 
                 degeneracy (Excl)
                         Degeneracy flag - controls input and analysis of degenerate sequence input (-D)
 
                 codon (Excl)
                         Codon Usage table to use for translation (-C)
 
                 order_by_cut (Switch)
                         Order the output by number of cuts/fragments (-c)
 
                 width (Integer)
                         Output width (between 60 and 210) (-w)
 
                 graphic (Excl)
                         Histogram output (-G)
 
                 binsize (Integer)
                         Step size in histogram
 
                 enzymes (String)
                         Enzymes selection list (separated by comma)
 
                 max_cut (Integer)
                         Maximum number of cuts allowed in sequence (-M)
 
                 min_cut (Integer)
                         Minimum number of cuts in sequence for the enzyme to be selected (-m)
 
                 magnitude (Excl)
                         Select enzymes by magnitude of recognition site (-n)
 
                 overhang (Excl)
                         Select enzymes by overhang generated (-o)
 
                 summary (Switch)
                         Summary of site information (-s)
 
                 print_fragments (Excl)
                         Table of fragments (-F)
 
                 sites (Switch)
                         Table of actual cut sites (a la Strider) (-S)
 
                 ladder_map (Switch)
                         Ladder map of selected enzymes (-l)
 
                 gel_map (Switch)
                         Pseudo-graphic gel map (-g)
 
                 cutoff (Integer)
                         Low-end cutoff in number of bases for gel map (>= 10) 
 
                 linear_map (Switch)
                         Linear map a la Strider (-L)
 
                 translation (Switch)
                         Linear co-translation  (-t,-T)
 
                 translation_frames (Excl)
                         Translation in how many frames
 
                 three_letter (Switch)
                         Translation in 3-letter code (-T)
 
                 orf (Switch)
                         Do an ORF analysis
 
                 frame (List)
                         Frames to search
 
                 min_size (Integer)
                         Min ORF size
 
                 pattern_search (Switch)
                         Do a pattern search (-p)
 
                 pattern (String)
                         Pattern (<30 IUPAC character)
 
                 errors (Integer)
                         Max number of errors that are tolerated (<6) (-p)
 
                 name (String)
                         Label of pattern
 
                 proximity (Switch)
                         Do a proximity search
 
                 distance (String)
                         Distance between factors
 
                 nameA (String)
                         Name of first factor (nameA)
 
                 nameB (String)
                         Name of second factor (nameB)
 
                 quiet (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 (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/tacg.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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