Provided by: libtfbs-perl_0.5.svn.20100421-1build1_amd64
TFBS::PatternGen::AnnSpec - a pattern factory that uses the AnnSpec program (version 2.1)
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
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).
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.