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.