MoAn - Motif Annealer

MoAn is a discriminative pattern finder capable of using a very large negative set to greatly improve its predictive power. It is capable of handling sequences that are not repeat masked given that the negative set is a representative sample of promoters from the organism examined. It is implemented in C and distributed under the Gnu General Public License.

It depends heavily on the Asap C libraries (Troels Marstrand) and by extension the ds_ssort library (Giovanni Manzini), but these come bundled with the source so no additional downloads should be necessary.

Download MoAn source code

Download documentation

Note that I have experienced problems compiling with GCC 4.3. I am working on this, but in the meantime 4.2 and 4.1 should work. If this is not your default open the Makefile in the MoAn directory in your favourite text editor and then change the line:

CC=gcc

to:

CC=gcc-4.2

and make sure you have it installed on your computer. In Ubuntu or Debian this can be done with the command:

sudo apt-get install gcc-4.2

Installing:

Compiling should simply be a simple matter of unpacking and running make:

tar xvzf moan_current.tar.gz
cd MoAn
make

Paper describing method:

Valen, E., Winther, O., Sandelin, A. and Krogh, A.
Discovery of regulatory elements is dramatically improved by a discriminatory approach.
PLoS Computational Biology 5(11) 2009

Studies using MoAn:

Liu, Y., Gao, H., Marstrand, T.T., Strom, A., Valen, E., Sandelin, A., Gustafsson, J.A. and Dahlman-Wright, K.
The genome landscape of ERα- and ERβ-binding DNA regions.
Proceedings of the National Academy of Sciences, 105(7) 2008.