tfbs::patterngen::gibbs::motif(3pm) [debian man page]

TFBS::PatternGen::Gibbs::Motif(3pm)			User Contributed Perl Documentation		       TFBS::PatternGen::Gibbs::Motif(3pm)

NAME

       TFBS::PatternGen::Gibbs::Motif - class for unprocessed motifs and associated numerical scores created by the Gibbs program

SYNOPSIS

DESCRIPTION

       TFBS::PatternGen::Gibbs::Motif is used to store and manipulate unprocessed motifs and associated numerical scores created by the Gibbs
       program. You do not normally want to create a TFBS::PatternGen::Gibbs::Motif yourself. They are created by running TFBS::PatternGen::Gibbs

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard and Wynand Alkema
       Boris Lenhard <Boris.Lenhard@cgb.ki.se> Wynand Alkema <Wynand.Alkema@cgb.ki.se>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore.

   MAP
	Title	: MAP
	Usage	: my $map_score = $motif->MAP;
	Function: returns MAP score for the detected motif
		  (This is a backward compatibility method. For consistency,
		   you should use $motif->tag('MAP_score') instead
	Returns : float (a scalar)
	Args	: none

   Other methods
       TFBS::PatterGen::Motif::Gibbs inherits from TFBS::PatternGen::Motif, which inherits from TFBS::Matrix. Please consult the documentation of
       those modules for additional available methods.

perl v5.14.2							    2008-01-24				       TFBS::PatternGen::Gibbs::Motif(3pm)

TFBS::PatternGen::Elph(3pm)				User Contributed Perl Documentation			       TFBS::PatternGen::Elph(3pm)

NAME

       TFBS::PatternGen::Elph - a pattern factory that uses the Elph program

SYNOPSIS

	   my $patterngen =
		   TFBS::PatternGen::Elph->new(-seq_file=>'sequences.fa',
						-binary => '/Elph/elph'
						-motif_length => [8, 9, 10],
						-additional_params => '-x -r -e');

	   my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object

DESCRIPTION

       TFBS::PatternGen::Gibbs builds position frequency matrices using an advanced Gibbs sampling algorithm implemented in external Gibbs program
       by Chip Lawrence. The algorithm can produce multiple patterns from a single set of sequences.

   new
	Title	: new
	Usage	: my $db = TFBS::PatternGen::Gibbs->new(%args);
	Function: the constructor for the TFBS::PatternGen::Gibbs object
	Returns : a TFBS::PatternGen::Gibbs object
	Args	: This method takes named arguments;
		   you must specify one of the following three
		   -seq_list	 # a reference to an array of strings
				 #   and/or Bio::Seq objects
		     # or
		   -seq_stream	 # A Bio::SeqIO object
		     # or
		   -seq_file	 # the name of the fasta file containing
				 #   all the sequences
		  Other arguments are:
		   -binary	 # a fully qualified path to Gibbs executable
				 #  OPTIONAL: default 'Gibbs'
		   -nr_hits	 # a presumed number of pattern occurences in the
				 #   sequence set: it can be a single integer, e.g.
				 #   -nr_hits => 24 , or a reference to an array of
				 #   integers, e.g -nr_hits => [12, 24, 36]
		   -motif_length # an expected length of motif in nucleotides:
				 #   it can be a single integer, e.g.
				 #   -motif_length => 8 , or a reference to an
				 #   array ofintegers, e.g -motif_length => [8..12]
		   -additional_params  # a string containing additional
				       #   command-line switches for the
				       #   Gibbs program

   pattern
   all_patterns
   patternSet
       The three methods listed above are used for the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
       TFBS::PatternGen for details.

perl v5.14.2							    2008-01-24					       TFBS::PatternGen::Elph(3pm)