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- PreMod: searches in whole genome alignments of hs/mm/rn for conserved matches of transfac-matrices in non-coding regions and predicts 100.000 enhancers on the human genomen, searchable, with nice displays.
- CisModScan: searches for clusters of binding sites
- BEARR lets you download sequences and searches for sites
- XCisClique searches for cluster of sites called Bicliques in Arabidopsis: Genes have to be co-expressed + share a combinatin of motifs. It works only on Arabidopsis.
- GALA lets you download multiz-alignments of human-mouse-rat, already scanned for conserved Transfac matrices at 0.85. There's a lot of filtering options available.
- cisView has the results of a whole-genome scan for TFBSs with patterns from the literature, Jaspar, Xie et al. They add a whole lot of analyzation, overrepresented distances, flanking genes, GOs of flanking genes. Regions can be narrowed down to conserved distal regions or proximal upstream promoters.
- CoMoDis searches mammalian alignments for matches to a given binding site model around a set of flanking sequence for a list of genes.
- Swissregulon: Alignments and predicted regulative features on GBrowse