Bio::Tools::Run::PiseApplication::tacg # 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)

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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.bioperl.org/ 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. This software is provided "as is" without warranty of any kind. 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.