FIRE-pro (Finding Informative Regulatory Elements in proteins) is a motif discovery and characterization program for proteins based on mutual information
BayesMD is a flexible, fully Bayesian model for motif discovery consisting of motif, background and alignment modules. BayesMD can be customized to different kind of biological applications, e.g. microarray, ChIP-chip, ditag, CAGE data analysis by integrating appropriately chosen features and functionalities.
Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences. Pscan does not resort to comparisons with orthologous sequences and experimental results show that it compares favorably to other tools for the same task in terms of false positive predictions and computation time.
Weeder is an algorithm for the automatic discovery of conserved motifs in a set of related regulatory DNA sequences.
WeederH is a software for finding of conserved nucleotide motifs and regions through comparative genomics, tailored for the analysis of non-coding DNA and the identification of conserved TFBSs or whole enhancers or silencers.
Allegro is a software tool for simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). Allegro is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.
Amadeus is a user-friendly software platform for genome-scale detection of known and novel motifs (recurring patterns) in DNA sequences, applicable to a wide range of motif discovery tasks. Amadeus outperforms extant tools and sets a new standard for motif discovery software in terms of accuracy, running time, range of application, wealth of output information and ease of use.
PhyloNet (Phylogenetic Regulatory Network) is a motif discovery program. It represents a very new paradigm for motif discovery: based on sequences of several evolutionarily related genomes, PhyloNet predicts a near complete set of conserved motifs of the organism of interest,as well as gene clusters that share these motifs, without reliance of additional data such as gene regulation.
::DEVELOPER
Stormo Lab in Department of Genetics, Washington University
Zagros is a motif discovery software for CLIP-Seq high-throughput protein-RNA interaction data. Given the regions of significant enrichment for reads Zagros can characterize the binding site for the given RBP. Zagros contains two additional programs to calculate the base pairing probabilities of the input sequences and extracting experiment specific events to incorporate such information for an extremely accurate motif discovery.
The XXmotif web server can discover motifs that are enriched in sets of nucleotide sequences provided by the user. XXmotif uses a new approach for finding enriched motifs: It directly optimizes the statistical significance of enrichment for PWMs. It can also score conservation and positional clustering of motifs. In several benchmarks on yeast and metazoan sequences, the underlying XXmotif method showed better sensitivity and produced PWMs of higher quality than state-of-the-art tools.