PRIORITY is a tool for de novo motif discovery in the context of transcription factor (TF) binding sites. It implements a new approach to motif discovery in which informative priors over sequence positions are used to guide the search.
GIMSAN (GIbbsMarkov with Significance ANalysis) is a web-server tool for de novo motif discovery:
Hybrid Gibbs sampler for motif finding that uses a Bayesian prior on the percentage of sequences containing sites but uses a maximum likelihood approach on the motif matrix
Biologically realistic and reliable statistical significance analysis
Using a 3-Gamma approximation scheme
Factoring local sequence composition information
Reports an approximate 95% confidence interval of the point estimator of the motif p-value
Can be used to select the optimal width from a range of motif widths based on our significance analysis
Column pair dependency estimated using a Monte-Carlo scheme
PriorsEditor is a general workbench for regulatory region analysis and transcription factor binding site discovery. The program emphasizes the use of positional priors to focus the search for binding sites towards portions of DNA sequences that are considered more likely to contain true functional sites. Positional priors tracks can be constructed by manipulating, comparing and combining information about various features, including for instance phylogenetic conservation, DNase hypersensitive sites, repeat regions, nucleosome positions and other epigenetic data, physical properties of the DNA helix, distance from transcription start site or proximity to other known binding sites and many more. Data can be downloaded from the UCSC Genome Browser (or imported from file) and visualized with the graphical user interface. It is also possible to perform de novo motif discovery or motif scanning with known motif models by interfacing with locally installed programs. The results can then be visualized, analyzed and post-processed within PriorsEditor.