| TFBS::PatternGen::AnnSpec(3pm) | User Contributed Perl Documentation | TFBS::PatternGen::AnnSpec(3pm) |
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.
Wynand Alkema <Wynand.Alkema@cgb.ki.se<gt>
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
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.
| 2022-10-20 | perl v5.36.0 |