Department of Computer Science
Enhancer Element Locator

Enhancer Element Locator

Enhancer Element Locator, or EEL, is a tool for locating distal gene enhancer elements in mammalian genomes by comparative genomics.

News

EEL is not dead! It is continually maintained and developed and new features will be published in due course. The latest public source code is available at github repository.

Database access

We have computed EEL alignments between orthologous genes from human and many other species. The results are available on our mysql server at http://tkt_bsap.staff.cs.helsinki.fi/EELweb/.

The data is regularly updated with some synchronization with ENSEMBL database, which we use as source of genomic information. The current database is also available via DAS service behind url http://tkt_bsap.staff.cs.helsinki.fi:10020.

Genome wide data download

The data used in the paper is available here along with up-to-date computations with more current genome assemblies.

Usage

Instructions for using the Enhancer Element Locator is available here. A straightforward protocol for EEL usage is also published in Nature Protocols.

Download

EEL version 1.1 has been updated to work on newer python versions, namely python 2.6 and 2.7. The new recommended source package is here. The previous installation and usage instructions still hold. The graphical Tcl/Tk interface or Windows platform have not been tested recently. This, and possibly later, EEL code can be found from the git repository.

The EEL-1.1 software for old python 2.4 is available for download in various forms under the GNU General Public Licence. Please use above, updated, package if you are using modern python environment. The following binary packages are still available for use on systems without standard python/numpy/C installation (especially Windows and Mac):

  1. Standalone Windows. Just install and use on Microsoft Windows.
  2. EEL-1.0 Compiled MacOS X. Compiled binary package for Apple/PowerPC users. No graphical user interface and needs either PYTHONPATH set or extracted in /System/ directory.
  3. EEL-1.0.1 Fancy MacOS X. For Apple/PowerPC users. Contains Mac specific graphical user interface.
  4. Compiled Windows. If you already have python installed on your computer, you can try this precompiled package with Python scripts.
  5. Source. This works with everyone with enough patience. For Linux users this is preferable distribution, others should be prepared for more or less work to get everything running (need at least C-compiler and Python). If you compile EEL on some system not listed above, please mail the binary package to Kimmo Palin.

Transcription factor motifs

You can obtain transcription factor motifs from databases such as JASPAR or use the motifs used in the CELL article.

Installation

Apple MacOS X

Download the version compiled for Mac OS X from here. Start the Terminal program and uncompress the package with command
tar -zxvf MacEEL-1.1.tar.gz
Follow the instructions in file EEL/MacEEL GUI INSTALL.rtf.

Linux and non-listed OSes

Download the source package from here. Uncompress the package by
tar -zxvf EEL-1.1.tar.gz
Finally go the EEL-1.1 directory and issue the command
python setup.py install
Now you should be able to launch eel with command
eel

Microsoft Windows

Click the link for standalone Windows EEL above and follow the instructions on the installer.

Updates


Kimmo Palin