| TOC for all levels |
| TFBS-0.5.0 | Top |
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| TFBS-0.5.0::Ext | Top |
| pwmsearch | Perl extension for scanning a DNA sequence object with a position weight matrix |
| TFBS-0.5.0::Ext::lib | Top |
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| TFBS-0.5.0::Ext::t | Top |
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| TFBS-0.5.0::examples | Top |
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| TFBS-0.5.0::examples::SAMPLE_FlatFileDir | Top |
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| TFBS-0.5.0::SCRIPTS | Top |
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| TFBS-0.5.0::t | Top |
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| TFBS-0.5.0::t::transfac_new | Top |
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| TFBS-0.5.0::t::transfac_old | Top |
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| TFBS-0.5.0::TFBS | Top |
| Matrix | 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 |
| 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. |
| SitePairSet | a set of TFBS::SitePair objects |
| SiteSet | a set of TFBS::Site objects |
| Word | base class for word-based patterns |
| TFBS-0.5.0::TFBS::Tools | Top |
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| TFBS-0.5.0::TFBS::PatternGen | Top |
| AnnSpec | a pattern factory that uses the AnnSpec program |
| Elph | a pattern factory that uses the Elph program |
| Gibbs | a pattern factory that uses Chip Lawrences Gibbs program |
| MEME | a pattern factory that uses the MEME program |
| SimplePFM | a simple position frequency matrix factory |
| YMF | a pattern factory that uses the MEME program |
| TFBS-0.5.0::TFBS::PatternGen::Motif | Top |
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| TFBS-0.5.0::TFBS::PatternGen::AnnSpec | Top |
| Motif | class for unprocessed motifs and associated numerical scores created by the Gibbs program |
| TFBS-0.5.0::TFBS::PatternGen::YMF | Top |
| Motif | class for unprocessed motifs and associated numerical scores created by the YMF program |
| TFBS-0.5.0::TFBS::PatternGen::Gibbs | Top |
| Motif | class for unprocessed motifs and associated numerical scores created by the Gibbs program |
| TFBS-0.5.0::TFBS::PatternGen::Elph | Top |
| Motif | class for unprocessed motifs and associated numerical scores created by the Gibbs program |
| TFBS-0.5.0::TFBS::PatternGen::MEME | Top |
| Motif | class for unprocessed motifs and associated numerical scores created by the Gibbs program |
| TFBS-0.5.0::TFBS::DB | Top |
| 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 |
| 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. ------------------------------------------------------------------------- |
| 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. ------------------------------------------------------------------------- |
| TFBS-0.5.0::TFBS::Matrix | Top |
| Alignment | class for alignment of PFM objects |
| ICM | class for information content matrices of nucleotide patterns |
| PFM | class for raw position frequency matrix patterns |
| PWM | class for position weight matrices of nucleotide patterns |
| TFBS-0.5.0::TFBS::Run | Top |
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| TFBS-0.5.0::TFBS::_Iterator | Top |
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| TFBS-0.5.0::TFBS::Word | Top |
| Consensus | IUPAC DNA consensus word-based pattern class |