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

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

NAME

       TFBS::PatternGen::SimplePFM - a simple position frequency matrix factory

SYNOPSIS

	   my @sequences = qw( AAGCCT AGGCAT AAGCCT
			       AAGCCT AGGCAT AGGCCT
			       AGGCAT AGGTTT AGGCAT
			       AGGCCT AGGCCT );
	   my $patterngen =
		   TFBS::PatternGen::SimplePFM->new(-seq_list=>@sequences);

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

DESCRIPTION

       TFBS::PatternGen::SimplePFM generates a position frequency matrix from a set of nucleotide sequences of equal length, The sequences can be
       passed either as strings, as Bio::Seq objects or as a fasta file.

       This pattern generator always creates only one pattern from a given set of sequences.

   new
	Title	: new
	Usage	: my $db = TFBS::PatternGen::SimplePFM->new(%args);
	Function: the constructor for the TFBS::PatternGen::SimplePFM
		   object
	Returns : a TFBS::PatternGen::SimplePFM obkect
	Args	: This method takes named arguments;
		   you must specify one of the following
		   -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

   pattern
   all_patterns
   patternSet
       The three above methods are used fro 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::SimplePFM(3pm)

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

NAME

       TFBS::PatternGen::AnnSpec - a pattern factory that uses the AnnSpec program (version 2.1)

SYNOPSIS

	   my $patterngen =
		   TFBS::PatternGen::AnnSpec->new(-seq_file=>'sequences.fa',
						   -binary => 'ann-spec '

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

DESCRIPTION

       TFBS::PatternGen::AnnSpec builds position frequency matrices using an external program AnnSpec (Workman, C. and Stormo, G.D.(2000) ANN-
       Spec: A method for discovering transcription factor binding sites with improved specificity. Proc. Pacific Symposium on Biocomputing 2000).

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Wynand Alkema
       Wynand Alkema <Wynand.Alkema@cgb.ki.se<gt>

   new
	Title	: new
	Usage	: my $pattrengen = TFBS::PatternGen::AnnSpec->new(%args);
	Function: the constructor for the TFBS::PatternGen::AnnSpec object
	Returns : a TFBS::PatternGen::AnnSpec 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 the 'meme' executable
				 #  OPTIONAL: default 'ann-spec'
		   -additional_params  # a string containing additional
				       #   command-line switches for the
				       #   ann-spec 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::AnnSpec(3pm)