ConservationProfile | |
DB | |
Matrix(1) | base class for matrix patterns, containing methods common
to all |
MatrixSet | an agregate class representing a set of matrix patterns, containing methods for manipulating the set as a whole |
PatternGen | a base class for pattern generators |
PatternGenI | |
PatternI | interface definition for all pattern objects (currently
includes matrices and word (consensus and regular expressions ) |
Site | a nucleotide sequence feature object representing (possibly putative) transcription factor binding site. |
SitePair | |
SitePairSet | a set of TFBS::SitePair objects |
SiteSet | a set of TFBS::Site objects |
TFFM | class for Transcription Factor Flexible Models (TFFMs) |
Word(1) | base class for word-based patterns |
_Iterator | |
FlatFileDir | interface to a database of pattern matrices
stored as a collection of flat files in a dedicated directory |
JASPAR2 | interface to MySQL relational database of pattern matrices |
JASPAR4 | interface to MySQL relational database of pattern matrices |
JASPAR5 | interface to MySQL relational database of pattern matrices. Currently status: experimental. |
JASPAR6 | interface to MySQL relational database of pattern matrices. Currently status: experimental. |
JASPAR7 | interface to MySQL relational database of pattern matrices. Currently status: experimental. |
LocalTRANSFAC | interface 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.
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TRANSFAC | interface 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.
------------------------------------------------------------------------- |