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MotifRegressor Software

The MotifRegressor software is based on the following paper:

Conlon, E.M., Liu, X.S., Lieb, J.D., Liu, J.S. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proceedings of the National Academy of Sciences USA, 100, 3339-3344.

Background

MotifRegressor: a program for finding DNA sequence motifs

MotifRegressor is a program written in the Perl programming language that automates the motif finding program "MDmodule" and the regression program "regressExpr.spl". It finds a group of motifs that are involved in the regulation of genes in one microarray experiment. MDmodule is provided as an executable program. MotifRegressor.pl and regressExpr.spl are provided as source code. Users can change this source code to specific needs, but cannot license any edited code for sale.

MotifRegressor requires the user to have the commercial statistical package Splus installed. MotifRegressor also relies in part on MDScan, a software package developed by the Brutlag Lab at Stanford University. For more information on MDScan, visit http://ai.stanford.edu/~xsliu/MDscan.

Obtaining Motif Regressor

The MotifRegressor software is available at no cost to academic users. Download the MotifRegressor software here:
Linux version Unix version

R version The R version was translated by Simon Drouin and Greg Finak, McGill University, Montreal, Canada. The R code works with both Linux and Unix; you first need to download the full packages for Linux and Unix above. Note: the R version gives different results than the Splus version.

Questions related to the application, use or installation of the software should be directed to Erin M. Conlon, University of Massachusetts, or X. Shirley Liu, Dana-Farber Cancer Institute.