Feb 152012

Allegro 1.0 / Amadeus 1.2


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.


Ron Shamir’s computational genomics group in Tel Aviv university.



  • Windows/Linux
  • Java


 Allegro / Amadeus



Allegro: Analyzing expression and sequence in concert to discover regulatory programs“,
Y. Halperin, C. Linhart, I. Ulitsky and R. Shamir,
Nucleic Acids Research, vol. 37:5, pp. 1566-1579, April 2009.

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.


Sorry, the comment form is closed at this time.