Tfsitescan is intended for promoter sequence analysis and works best with sequences of ~500 nt
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TFBIND for online searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)). This tool uses weight matrix in transcription factor database TRANSFAC R.3.4 developed by Dr. Wingender et al, and the cut-offs originally estimated by our research.
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TRAP (from Max Planck Isntitute of Molecular genetics) is a web tool to predict which transcription factors are susceptible to bind a DNA sequence (e.g. promotor of a gene of interest)
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PROMO (from Universitat Politècnica de Catalunya) from is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files. PROMO is using version 8.3 of TRANSFAC.
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analysis of transcription factor binding sites
Category: Transcription factors analysis
DiRE (Distant Regulatory Elements of co-regulated genes) uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the use
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Lasagna search is an integrated user friendly web tool for transcription factor binding site search and visualization.
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high-throughput discovery of functional regulatory elements
Category: Transcription factors analysis
Finding potential regulatory elements in noncoding regions of the human genome is a challenging problem. Analyzing novel sequences for the presence of known transcription factor binding sites or their weight matrices produces a huge number of false positive predictions that are randomly and uniformily distributed. rVista combines database searches with comparative sequence analysis, reducing the number of false positive predictions by ~95% while maintaining a high sensitivity of the search.
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PASTAA is a web app to evaluate if there is a regulatory association between transcription factors and groups of genes. Input: List of gene IDs.
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sTRAP (Transcription factor Affinity Prediction) is a web application to calculate how the binding of different TFs is affected by the sequence differences (e.g. by single-nucleotide polymorphism)
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TRAP (multiple sequences) is a web tool to evaluate which TFs are over represented in a data set (Chip-seq or Chip-chip data).
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Which sequence is more susceptible to be bound to your transcription factor represented by your matrix? Input data: Multiple DNA sequences, personal matrix.
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