fdrMotif is iterative and alternates between updating the position weight 
matrix (PWM) and significance testing. It starts with an initial PWM and a 
set of sequences (e.g., from ChIP experiments). It generates many sets of 
background (null) sequences under the input sequence probability model. At 
each model estimation step, fdrMotifs determines the number of binding sites 
in each sequence by performing statistical tests.  The FDR in the original 
dataset is controlled by monitoring the proportion of background subsequences 
that are declared as binding sites. The PWM is updated using an EM algorithm 
with two iterative steps (the E and M steps) until convergence. In the E-step, 
fdrMotif normalizes the sum of the probabilities over all positions in a 
sequence to the number of binding sites found in the sequence.

This program was developed by Yu Liang and Leping Li of the National Institutes of 
Environmental Health Sciences, Research Triangle Park, North Carolina 27709.


INSTALLATION

In the main directory of the distribution, type

./configure

then

make

make install

By default, the configure program will direct the executable files to 
/usr/local/bin which, in most cases, requires the user to "su" to root 
prior to the "make install" step. The target directory for the executable 
file can be overridden by specifying the --prefix option during the 
configure phase. For example,

./configure --prefix=/home/fdrMotif_user

will direct the executables into /home/fdrMotif_user/bin directory.

The configure application accepts several arguments to tailor the build 
and installation process. Please see the INSTALL file contained in the root 
directory of the distribution for further details.

The source code and package were developed using Windows and tested on 
Linux (Fedora). Although the intent was to make the code portable to most U*IX 
variants, you may encounter minor build issues on other platforms. Feedback 
regarding any difficulties you may experience will be very helpful in improving 
the distribution package. 


CONTACT

Leping Li, NIEHS
Phone: 919-541-5168
Email: li3@niehs.nih.gov

Robert Bass, NIEHS
Phone: 919-541-7594
Email: bass1@niehs.nih.gov

Yu Liang, SAS Institute
Phone: 919-677-8000
Email: Yu.Liang@sas.com
