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 v5.10.1 2008-01-24 TFBS::PatternGen::SimplePFM(3pm)