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

Langue: en

Autres versions - même langue

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

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::Tools::Run::PiseApplication::assp

SYNOPSIS

   #

DESCRIPTION

Bio::Tools::Run::PiseApplication::assp 
       Bioperl class for:
 
         ASSP    Accuracy of Secondary Structure Prediction (Russell, Barton)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/assp.html 
          for available values):
 
 
                 assp (String)
 
                 aligfile (InFile)
                         Alignement File (in BLOCK format)
 
                 clus2blc (Switch)
                         Convert CLUSTAL NBRF-PIR format to AMPS Blockfile format
 
                 nbrf_file (String)
 
                 showpar (Switch)
                         show all the parameters for the current run.
 
                 quiet (Switch)
                         avoid all output in the program except for errors and a final lower limit for Q3
 
                 matrix (InFile)
                         -m property type matrix file name
 
                 subsize (Integer)
                         -s length of sequence used to determine poor alignment
 
                 maxalig (Integer)
                         -l maximum number of sub-alignments to be considered
 
                 minprop (Integer)
                         -p minimum number or properties shared to define conservation
 
                 window (Integer)
                         -w window length for conservation definition
 
                 ignseq (Integer)
                         -i fraction of sequences that may be ignored
 
                 mingap (Integer)
                         -g minimum number of gaps allowed
 
                 seqomit (String)
                         -o Seq. to be omitted 1 Seq. to be omitted 2 ...

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/assp.html
•
Bio::Tools::Run::PiseApplication
•
Bio::Tools::Run::AnalysisFactory::Pise
•
Bio::Tools::Run::PiseJob

new

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