Programs |
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Match is a weight matrix-based program for predicting transcription factor binding sites (TFBS) in DNA sequences. It uses a library of positional weight matrices from TRANSFAC® Public 6.0. |
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F-Match is a program for identifying statistically over-represented transcription factor binding sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency. The program reads FASTA DNA sequence entries for the query and control sets. F-Match uses the Match algorithm and a library of positional weight matrices from TRANSFAC®6.0 to scan the input sequences in the two sets for putative TFBSs then compares the experimental and control sets to identify the statistically over-represented TFBSs. |
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Patch is a pattern-based program for predicting transcription factor binding sites (TFBS) in DNA sequences. It uses the set of binding sites from TRANSFAC® Public 6.0. |
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P-Match is a program for predicting transcription factor binding sites (TFBS) in DNA sequences that combines pattern matching and weight matrix approaches. It uses a library of positional weight matrices from TRANSFAC® Public 6.0 along with the site alignments associated with these matrices. Note that unlike Match, P-Match can only use the subset of the matrix libraries for which site alignments are. The algorithm is provided here as a standalone online application, working with only a snapshot of TRANSFAC® positional weight matrices and site alignments from 2005. For a modest academic/non-profit price, subscription to the ExPlain™ analysis platform provides access to a P-Match tool that works with the complete up-to-date library of TRANSFAC® positional weight matrices and their aligned binding sites. Learn more about the ExPlain™ analysis platform. |
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AliBaba2 is a program, developed by Niels Grabe, for predicting binding sites of transcription factor binding sites in an unknown DNA sequence using binding sites from TRANSFAC® Public. |
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Composite Module Analyst (CMA) 1.0 The CMA algorithm reads the output of the Match program and applies a genetic algorithm in order to define promoter models based on the composition of transcription factor binding sites and their pairs. |
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Search for TRANSFAC® Public transcription factors by molecular weight. |
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The MatrixCatch algorithm searches for potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence. MatrixCatch uses a library of CE matrix models compiled on the basis of experimentally identified CEs collected in TRANSCOMPEL Public and positional weight matrices for single TF-binding sites collected in TRANSFAC® 6.0 Public. |
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The SignalScan algorithm, developed by D. Prestridge, analyzes DNA sequences for known eukaryotic signals. |
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Search the S/MARtDB™ database by sequence. |
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Search the TRANSFAC® Public Factor Table by protein sequence. |
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