TOC for all levels
TFBS
TFBS::_Iterator
TFBS::DB
TFBS::Matrix
TFBS::PatternGen
TFBS::PatternGen::AnnSpec
TFBS::PatternGen::Elph
TFBS::PatternGen::Gibbs
TFBS::PatternGen::MEME
TFBS::PatternGen::Motif
TFBS::PatternGen::YMF
TFBS::Run
TFBS::Tools
TFBS::Word
TFBSTop
ConservationProfile
DB
Matrix(1)base class for matrix patterns, containing methods common to all
MatrixSetan agregate class representing a set of matrix patterns, containing methods for manipulating the set as a whole
PatternGena base class for pattern generators
PatternGenI
PatternIinterface definition for all pattern objects (currently includes matrices and word (consensus and regular expressions )
Sitea nucleotide sequence feature object representing (possibly putative) transcription factor binding site.
SitePair
SitePairSeta set of TFBS::SitePair objects
SiteSeta set of TFBS::Site objects
TFFMclass for Transcription Factor Flexible Models (TFFMs)
Word(1)base class for word-based patterns
_Iterator
TFBS::_IteratorTop
_MatrixSetIterator
_SiteSetIterator
TFBS::DBTop
FlatFileDirinterface to a database of pattern matrices stored as a collection of flat files in a dedicated directory
JASPAR2interface to MySQL relational database of pattern matrices
JASPAR4interface to MySQL relational database of pattern matrices
JASPAR5interface to MySQL relational database of pattern matrices. Currently status: experimental.
JASPAR6interface to MySQL relational database of pattern matrices. Currently status: experimental.
JASPAR7interface to MySQL relational database of pattern matrices. Currently status: experimental.
LocalTRANSFACinterface to local transfac database position frequency matrices (matrix.dat) -------------------------------- NOTICE ---------------------------------- The TRANSFAC database is free for non-commercial use. For commercial use the TRANSFAC databases and programs have to be licensed. Please read the DISCLAIMER at http://transfac.gbf.de/TRANSFAC/disclaimer.htm. -------------------------------------------------------------------------
TRANSFACinterface to database of TRANSFAC public position frequency matrices at TESS (http://www.cbil.upenn.edu/tess) -------------------------------- NOTICE ---------------------------------- The TRANSFAC database is free for non-commercial use. For commercial use the TRANSFAC databases and programs have to be licensed. Please read the DISCLAIMER at http://transfac.gbf.de/TRANSFAC/disclaimer.htm. -------------------------------------------------------------------------
TFBS::MatrixTop
Alignmentclass for alignment of PFM objects
ICMclass for information content matrices of nucleotide patterns
PFMclass for raw position frequency matrix patterns
PWMclass for position weight matrices of nucleotide patterns
_Alignment
TFBS::PatternGenTop
AnnSpeca pattern factory that uses the AnnSpec program (version 2.1)
Elpha pattern factory that uses the Elph program
Gibbsa pattern factory that uses Chip Lawrences Gibbs program
MEMEa pattern factory that uses the MEME program
SimplePFMa simple position frequency matrix factory
YMFa pattern factory that uses the MEME program
TFBS::PatternGen::AnnSpecTop
Motif(1)class for unprocessed motifs and associated numerical scores created by the Gibbs program
TFBS::PatternGen::ElphTop
Motif(2)class for unprocessed motifs and associated numerical scores created by the Gibbs program
TFBS::PatternGen::GibbsTop
Motif(3)class for unprocessed motifs and associated numerical scores created by the Gibbs program
TFBS::PatternGen::MEMETop
Motif(4)class for unprocessed motifs and associated numerical scores created by the Gibbs program
TFBS::PatternGen::MotifTop
Matrix(2)
Word(2)
TFBS::PatternGen::YMFTop
Motif(5)class for unprocessed motifs and associated numerical scores created by the YMF program
TFBS::RunTop
ConservationProfileGenerator
TFBS::ToolsTop
SetOperations
TFBS::WordTop
ConsensusIUPAC DNA consensus word-based pattern class