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Download
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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/
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.
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 |
Chicken.masked_promoters.Ensembl_v69.zip
| 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 |
| Solanum lycopersicum (Tomato) |
Ensembl Plants |
July '17 |
11,720 |
9.3 MB |
| Solanum tuberosum (Potato) |
Spud DB |
Oct '20 |
17,981 |
6.7 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.
* 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.
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