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  • AmadeusPBM v1.0

    AmadeusPBM v1.0  with Allegro v1.0 and Amadeus v1.2 (12 Jul 2011)
    Follow this link to download the files necessary to execute AmadeusPBM/Allegro/Amadeus.
    You will also need to download regulatory sequences for the organism(s) you are analyzing or PBM file in case you are using AmadeusPBM - see below.

    This version includes Amadeus, Allegro and AmadeusPBM. AmadeusPBM allows reconstruction of binding site motifs from protein binding microarray (PBM) data.
    Amadeus PBM is built on top of Allegro and has the same operating systems and hardware specifications. Additional hardware and software requirements, as well as detailed instructions on how to execute the program, are found in README.txt file in the download package in the overview page.
    An example of a PBM dataset is available below (under "PBM data"). More PBM files can be downloaded from http://the_brain.bwh.harvard.edu/uniprobe/.
    The software gets a PBM filename, scoring scheme to choose, k as the length of the k-mer to work on, and how many k-mers to treat as a target set. The output is a binding site in PWM logo and a list of similar PWMs from jaspar or transfac.

    Amadeus/Allegro is a Java application. It requires Java 1.5 and at least 1GB RAM memory. Allegro should run properly on Windows (2000/XP/Vista) and Linux (Debian). It was not tested on Mac OS. Additional hardware and software requirements, as well as detailed instructions on how to execute the program, are found in the README.txt file in the download package and in the overview page.

    The AmadeusPBM/Allegro/Amadeus software is freely available for academic use. It is also available for non-academic use under appropriate licensing. Please contact Ron Shamir (rshamir AT post.tau.ac.il) or Chaim Linhart (chaiml AT post.tau.ac.il) for further information.


  • Known regulatory motifs from public databases

    Please extract the zip files into the Allegro/Amadeus installation directory.
    Each zip file contains a folder with known regulatory motifs from public database.
    After unzipping:
    • The miRBase files should reside under [installation_dir]/data/miRNA/
    • The JASPAR folder should reside under [installation_dir]/data/TFs/.

  • The PLACE PWMs should reside under [installation_dir]/data/TFs/.
    AMADEUS/ALLEGRO interfaces with the PLACE PWMs data, which is available under "PLACE National Institute of Agrobiological Sciences licensed under CC Attribution-Share Alike 2.1 Japan" licnese.

Promoter analysis with JAPSAR PWMs:
    Please change the "Known motifs DB" field in AMADEUS to the prefered JASPAR PWMs file under [installation_dir]/data/TFs/JASPAR/

Regulator type Source Version File size
micro-RNA miRBase 21.0 NEW 953 KB
Transcription Factor JASPAR 5.0_ALPHA NEW 167 KB
Transcription Factor PLACE Jan 2007NEW 127 KB

  • Regulatory sequences

    Please extract the zip files into the Allegro/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]/Allegro_v1.0/data/sequences/[organism]/.
    All sequences are repeat masked, unless indicated otherwise.

    Chicken.masked_promoters.Ensembl_v69.zip
    Promoters *
    Organism Source Version # genes File size
    Human Ensembl Jan '16 (v75, GRCh37) NEW 19,353 12.5 MB
    Chimpanzee Ensembl Apr '13 (69) 17,100 10.4 MB
    Dog Ensembl Apr '13 (69) 19,571 12.8 MB
    Mouse Ensembl Apr '13 (v69, NCBI m37) 19,851 14.0 MB
    Rat Ensembl Feb '6 (v83, Rnor_6.0) NEW 15,923 11.7 MB
    Rat Ensembl Apr '13 (v69, RGSC 3.4) 23,197 12.1 MB
    Chicken Ensembl Apr '13 (69) 15,308 11.5 MB
    Zebrafish Ensembl Apr '13 (69) 15,259 10.4 MB
    Fruitfly Ensembl Apr '13 (69) 12,267 10.7 MB
    C. elegans Ensembl Apr '13 (69) 20,502 15.6 MB
    S. cerevisiae Ensembl Nov '12 (68) 6,664 1.9 MB
    Sorghum Bicolor Ensembl Plants Jan '13 36,410 18.8 MB
    S. pombe PomBase Nov '12 4,694 4.2 MB
    Arabidopsis TAIR Nov '12 33,602 22.8 MB
    O. Sativa Japonica (Rice) Ensembl Gramene Dec '15 29,083 20.8 MB
    * Sequences extracted from the Ensembl project include 3 Kb upstream of the TSS, and the first two exons and introns. As of release 69, promoter sequences were downloaded via BioMart, and include 3 Kb upstream and the 5' utr.
    Sequences for Sorghum Bicolor organism include 2 Kb upstream of the TSS.

    3' UTRs *
    Organism Source Version # genes File size
    Human Ensembl Jun '13 (71) 19,605 8.3 MB
    Mouse Ensembl Jun '13 (71, mm9) 20,004 7.3 MB
    Mouse Ensembl Aug '15 (81, mm10) 19,898 6.2 MB
    Arabidopsis TAIR Jun '13 20,345 1.7 MB
    O. Sativa Japonica (Rice) Ensembl Gramene Dec '15 29,382 4.2 MB
    * As of release 71 of Ensembl, 3' UTR sequences were downloaded via BioMart. For genes with more than one sequence, the longest 3' UTR was selected.

    PBM data
    Organism Source File size
    Mouse Uniprobe 1.67 MB