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.