Bio::Tools::Run::PiseApplication::most.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::most

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::most
       Bioperl class for:
 
         MoST    Motif Search Tool (Tatusov, Altschul, Koonin)
 
       Parameters:
 
 
                 most (Excl)
                         MoST program
 
                 cap (Paragraph)
                         CAP Parameters
 
                 blast_output (InFile)
                         Blast Output File
 
                 capoutfile (OutFile)
                         CAP result file
 
                 criterium (Excl)
                         Criterium
 
                 noless (Integer)
                         min height of motif (%)
 
                 blast_score (Integer)
                         min Blast score
 
                 mostopt (Paragraph)
                         MoST Parameters
 
                 aadb (Excl)
                         Protein Database
 
                 block (InFile)
                         Block file (generated by CAP)
 
                 iter (Integer)
                         how many iterations
 
                 method (Excl)
                         Method of computation of position-dependent weight matrix from alignment block
 
                 seg (Switch)
                         apply seg filter
 
                 segv (Integer)
                         width parameter (if segfilter)
 
                 identical (Integer)
                         use only one representative of each group of sequence segments that are #% or more identical
 
                 tmpfile (Results)
 
 

new

  Title   : new()
  Usage   : my $most = Bio::Tools::Run::PiseApplication::most->new($remote, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::most object.
            This method should not be used directly, but rather by 
            a Bio::Factory::Pise instance:
            my $factory = Bio::Factory::Pise->new(-email => 'me@myhome');
            my $most = $factory->program('most');
  Example :
  Returns : An instance of Bio::Tools::Run::PiseApplication::most.