REDUCE Suite v2.0 Homepage

Introduction

We are pleased to announce the release of the REDUCE Suite v2.0, a set of software tools to model the regulation of gene expression by transcription factors (TF). By directly correlating genome-wide mRNA expression or TF binding data (e.g. ChIP-chip) with associated nucleotide sequences, the REDUCE Suite can discover the sequence-specific binding affinity of a TF from a single experiment, using all measurements simultaneously, and without using any "background" sequence model.

The REDUCE Suite of software programs has been developed and actively maintained by the Laboratory of Dr. Harmen Bussemaker at the Department of Biological Sciences, Columbia University in the City of New York. The suite has its origin in the REDUCE algorithm of Bussemaker, Li, and Siggia, Nature Genetics (2001), which pioneered the use of motif-based linear regression model to discover cis-regulatory elements (motifs) and infer condition-specific transcription factor activities from a single genomewide mRNA expression profile. Dr. Barrett Foat, a former graduate student in the Bussemaker Lab, extended REDUCE by adding an optimization procedure to obtain a so-called Position Specific Affinity Matrix (PSAM). He implemented his algorithm in a new program, MatrixREDUCE, using Perl and GNU Scientific Library (GSL). Dr. Xiang-Jun Lu, a current Senior Research Associate in the Bussemaker Lab, has completely rewritten and significantly enhanced the code using pure ANSI C (with Numerical Recipes routines) to make each component program efficient and the whole package self-contained.

Following the release of MatrixREDUCE v1.0 in late 2006, we have made many significant additions and improvements to the software based on extensive feedback from within and outside the lab. Specially, we have greatly improved the calculation of P-values based on a heuristic null model described in Foat, Tepper, and Bussemaker, NAR (2008), and developed a versatile topology-based approach to specify motif patterns. Moreover, we have implemented MotifREDUCE as a standalone, yet more robust and efficient, replacement of the original REDUCE program, and created a command-line driven, general-purpose DNA/RNA-related LogoGenerator. Overall, the suite now consists of more than ten standalone, yet interconnected programs. To better reflect both its root and new versatile functionality, the package has been renamed the "REDUCE Suite", currently at version 2.0. Note that while now superseded by the REDUCE Suite, MatrixREDUCE v1.0 is still available.

We understand that getting a scientific software tool published is just the beginning; in the long run, it is the continuous refinements and adaption to the changing world that make a software suite alive. So while standard "no warranty" applies, we stand firmly behind the REDUCE Suite. We strive to get back to your questions, suggestions and bug reports quickly and concretely.

REDUCE Suite Forum

Welcome to the REDUCE Suite! We have created a forum for REDUCE Suite related topics. Please see the release note.

Registration

You must accept our license terms and register first before you can download and use the REDUCE Suite software package.

Download the package

Please register first (see above). You can then download either the source code and/or pre-compiled binary distribution for Linux, Mac OS X (Intel), Mac OS X (PPC), Cygwin (Windows), MinGW/MSYS for native Windows, and Sun OS.

Installation

Please following instruction "Installation and setup" at the forum.