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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.