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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.