The Amadeus motif discovery platform

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.

PBM analysis: Amadeus can be used to identify binding site motifs from Protein Binding Microarray (PBM) data. A PBM dataset of a specific TF includes its measured binding intensities for each probe sequence covering together all possible 10-mers. In a blind competition (DREAM5 Challenge, Sep. '10) Amadeus ranked first (tied with one other group) in identifying the binding site motifs of 66 TF datasets. Running time is a few seconds per dataset.

Note: Amadeus is now integrated with Allegro, our new motif-finding algorithm for discovering transcriptional modules in gene expression datasets. Revisions are made only to the combined Amadeus/Allegro version. Visit the Allegro web-site for more details and for the latest software and data.

Amadeus is described in our paper:
"Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets", C. Linhart, Y. Halperin and R. Shamir,
Genome Research, vol. 18:7, pp. 1180-1189, July 2008.

Amadeus-PBM is described in our paper:
"Assessment of Algorithms for Inferring Positional Weight Matrix Motifs of Transcription Factor Binding Sites Using Protein Binding Microarray Data", Y. Orenstein, C. Linhart and R. Shamir,
PLoS ONE, vol. 7(9), September 2012.

Screenshot of Amadeus   (click on image for full-size version)

This web-site contains the following:

• The AMADEUS motif finding software
  The overview page explains how to run Amadeus and read its output.
  The download page contains the Amadeus software and files with regulatory sequences (promoters and 3' UTRs) of various organisms in Amadeus-compatible format. Amadeus is freely available for academic use.
  
  
• Compendium of metazoan TF and miRNA target sets
  We collected from the literature a large-scale compendium of transcription factor and microRNA target gene sets derived from diverse high-throughput experiments (mainly gene expression microarrays and ChIP-chip assays) in several metazoans. This compendium can be used as a benchmark for motif discovery tools, and for studying properties of TF/miRNA targets.
  
  
• Supplementary data for our Genome Research paper
  The supplementary data includes a detailed description of our TF/miRNA target-sets compendium, and results of Amadeus and other motif finders in our benchmark experiment.