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Bioinformatics Advance Access published online on April 8, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn126
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

A system for generating transcription regulatory networks with combinatorial control of transcription

Sushmita Roy a, Margaret Werner-Washburne b and Terran Lane a,*

Dept. of Computer Sciencea and Biologyb, University of New Mexico, Albuquerque, NM 87131

*To whom correspondence should be addressed. Dr. Terran Lane, E-mail: terran{at}cs.unm.edu


  Abstract

Summary We have developed a new software system, REgulatory Network generator with COmbinatorial control (RENCO), for automatic generation of differential equations describing pretranscriptional combinatorics in artificial regulatory networks. RENCO has the following benefits: (a) it explicitly models protein-protein interactions among transcription factors, (b) it captures combinatorial control of transcription factors on target genes, and (c) it produces output in Systems Biology Markup Language (SBML) format, which allows these equations to be directly imported into existing simulators. Explicit modeling of the protein interactions allows RENCO to incorporate greater mechanistic detail of the transcription machinery compared to existing models and can provide a better assessment of algorithms for regulatory network inference.

Availability: RENCO is a C++ command line program, available at http://sourceforge.net/projects/renco/

Associate Editor: Dr. Limsoon Wong

Received on January 21, 2008; revised on March 13, 2008; accepted on April 4, 2008

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