📦 libtfbs-perl

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• TFBS::DB::FlatFileDir(3pm)interface to a database of pattern matrices stored as a collection of flat files in a dedicated directory✨
• TFBS::DB::JASPAR(3pm)interface to MySQL relational database of pattern matrices. Currently status: experimental.✨
• TFBS::DB::JASPAR2(3pm)interface to MySQL relational database of pattern matrices✨
• TFBS::DB::JASPAR4(3pm)interface to MySQL relational database of pattern matrices✨
• TFBS::DB::JASPAR5(3pm)interface to MySQL relational database of pattern matrices. Currently status: experimental.✨
• TFBS::DB::JASPAR6(3pm)interface to MySQL relational database of pattern matrices. Currently status: experimental.✨
• TFBS::DB::JASPAR7(3pm)interface to MySQL relational database of pattern matrices. Currently status: experimental.✨
• TFBS::DB::LocalTRANSFAC(3pm)interface to local transfac database position frequency matrices (matrix.dat)✨
• TFBS::DB::TRANSFAC(3pm)interface to database of TRANSFAC public position frequency matrices at TESS (http://www.cbil.upenn.edu/tess)✨
• TFBS::Ext::pwmsearch(3pm)Perl extension for scanning a DNA sequence object with a position weight matrix✨
• TFBS::Matrix(3pm)base class for matrix patterns, containing methods common to all✨
• TFBS::Matrix::Alignment(3pm)class for alignment of PFM objects✨
• TFBS::Matrix::ICM(3pm)class for information content matrices of nucleotide patterns✨
• TFBS::Matrix::PFM(3pm)class for raw position frequency matrix patterns✨
• TFBS::Matrix::PWM(3pm)class for position weight matrices of nucleotide patterns✨
• TFBS::MatrixSet(3pm)an agregate class representing a set of matrix patterns, containing methods for manipulating the set as a whole✨
• TFBS::PatternGen(3pm)a base class for pattern generators✨
• TFBS::PatternGen::AnnSpec(3pm)a pattern factory that uses the AnnSpec program (version 2.1)✨
• TFBS::PatternGen::AnnSpec::Motif(3pm)class for unprocessed motifs and associated numerical scores created by the Gibbs program✨
• TFBS::PatternGen::Elph(3pm)a pattern factory that uses the Elph program✨
• TFBS::PatternGen::Elph::Motif(3pm)class for unprocessed motifs and associated numerical scores created by the Gibbs program✨
• TFBS::PatternGen::Gibbs(3pm)a pattern factory that uses Chip Lawrences Gibbs program✨
• TFBS::PatternGen::Gibbs::Motif(3pm)class for unprocessed motifs and associated numerical scores created by the Gibbs program✨
• TFBS::PatternGen::MEME(3pm)a pattern factory that uses the MEME program✨
• TFBS::PatternGen::MEME::Motif(3pm)class for unprocessed motifs and associated numerical scores created by the Gibbs program✨
• TFBS::PatternGen::SimplePFM(3pm)a simple position frequency matrix factory✨
• TFBS::PatternGen::YMF(3pm)a pattern factory that uses the MEME program✨
• TFBS::PatternGen::YMF::Motif(3pm)class for unprocessed motifs and associated numerical scores created by the YMF program✨
• TFBS::PatternI(3pm)interface definition for all pattern objects (currently includes matrices and word (consensus and regular expressions )✨
• TFBS::Site(3pm)a nucleotide sequence feature object representing (possibly putative) transcription factor binding site.✨
• TFBS::SitePair(3pm)✨
• TFBS::SitePairSet(3pm)a set of TFBS::SitePair objects✨
• TFBS::SiteSet(3pm)a set of TFBS::Site objects✨
• TFBS::TFFM(3pm)class for Transcription Factor Flexible Models (TFFMs)✨
• TFBS::Word(3pm)base class for word-based patterns✨
• TFBS::Word::Consensus(3pm)IUPAC DNA consensus word-based pattern class =head1 DESCRIPTION✨