Home 
Amadeus home  
Overview 
Amadeus software overview  
Download 
Download Amadeus and the compendium  
Supplementary data 
Supplementary data for the paper  
Contact us 


Download 

    • Software:
      NEW:       Amadeus v1.2 with Allegro (21 Dec 2008) Amadeus v1.2 is integrated with Allegro, our new motif-finding algorithm for discovering transcriptional modules in gene expression datasets.

      Previous version:
      Amadeus v1.1  with miRBase 12.0 (12 Oct 2008)
      Follow this link to download the files necessary to execute Amadeus.
      You will also need to download sequences for the organism(s) you are analyzing - see below.

    • miRBase 12.0: (for users who downloaded Amadeus before 12 Oct 2008)
      Please download miRBase12.0.zip and extract it into the Amadeus v1.1 installation directory. The zip file contains files with matrices of micro-RNA seeds, based on the miRBase database, release 12.0 (Sep 2008). These matrices are used by Amadeus in 3' UTR analysis to compare the motifs it discovers to seeds of known micro-RNAs. The new matrices replace those in the old Amadeus v1.1 installation, which were based on miRBase release 10.0.
      After unzipping, the files should reside under [installation_dir]/Amadeus_v1.1/data/miRNA/.
      For some of the popular species, or groups of species, we prepared matrix files with only the relevant micro-RNAs, as detailed in the README.txt file.

    • Sequences:
      The sequence files are now maintained in the Allegro download page.

      After downloading the zip file, please extract it into the Amadeus installation directory.
      Each zip file contains a file with promoter/3'-UTR sequences, and a corresponding background-set file. After unzipping, the files should eventually reside under [installation_dir]/Amadeus_v1.1/data/sequences/[organism]/.


  • Metazoan compendium  (15 Apr 2008, 57.3 KB)
    TF and miRNA target sets in human, mouse, fruit-fly and C. elegans, collected from the literature. This compendium was used as a benchmark to compare the success rate and running time of Amadeus and other motif discovery tools.
    Each file contains a single target set, given as a list of Ensembl gene ids.
    Full description of the compendium can be found at the supplementary data page.