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
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.
