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/MailList.shtml  - 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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

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/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.