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. |
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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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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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3DTF: Transcription factor PWMs from 3D structure-based energy calculations 3DTF is a program to analyze the protein-DNA binding site and calculate Positional weight matrix (PWM), representing the DNA-binding specifity of the protein. |
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m2match - Transfac Motif comparison tool The m2match algorithm was designed for the pairwise comparison of DNA sequence motifs described by Positional Frequency Matrices (PFMs). This webserver enables two applications, motif search and motif clustering. |
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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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VCFmerge is a user friendly online interface based on tabix, bgzip, and vcftools. It allows you to upload VCF files of single samples (either in raw or in compressed form) and combine them into a single VCF file that contains all the samples, which you can download. |
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