Bio::Tools::Run::PiseApplication::lassap.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::lassap

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::lassap
       Bioperl class for:
 
         LASSAP  LArge Scale Sequence compArison Package (Glemet, Codani)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/lassap.html 
          for available values):
 
 
                 lassap (String)
 
                 method (Excl)
                         Comparison method
 
                 dna_comp (Switch)
                         nucleic/nucleic comparison
 
                 query1 (Sequence)
                         First sequence
 
                 query2 (Sequence)
                         Second sequence
 
                 dr1 (String)
 
                 dr2 (String)
 
                 matrix (Excl)
                         Scoring matrix
 
                 gapo (Integer)
                         Gap open penalty
 
                 gape (Integer)
                         Gap extension penalty
 
                 cutoff (Integer)
                         Cutoff
 
                 Expect (Integer)
                         Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (E)
 
                 E2 (Integer)
                         E2 (expected number of HSPs that will be found when comparing two sequences that each have the same length)
 
                 S2 (Integer)
                         S2 (cutoff score which defines HSPs)
 
                 W (Integer)
                         W (length of words identified in the query sequence)
 
                 T (Integer)
                         T (neighborhood word score threshold)
 
                 X (Integer)
                         X (word hit extension drop-off score)
 
                 ktup (Integer)
                         ktup : sensitivity and speed of the search
 
                 init1 (Switch)
                         sequences ranked by the z-score based on the init1 score
 
                 noopt (Switch)
                         no limited optimization
 
                 linlen (Integer)
                         output line length for sequence alignments (< 200)
 
                 ran (Integer)
                         How many randomizations
 
                 swap (Switch)
                         Don't test for inclusion of query1 into query2
 
                 k (Integer)
                         How many best alignments
 
                 frame_query1 (List)
                         First sequence frames
 
                 frame_query2 (List)
                         Second sequence frames
 
                 gc (Excl)
                         Genetic Code
 
                 view_alignment (Switch)
                         View alignment (not available for all methods)
 
                 scut (Integer)
                         Score cutoff
 
                 pcut (Integer)
                         Probability cutoff
 
                 max (Integer)
                         Maximum retained
 
                 flag_algo_opt (String)
 
                 flag_algo_opt2 (String)
 
                 gc2 (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/lassap.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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