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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.