CplexA: a Mathematica package to study macromolecular-assembly control of gene expression

TL;DR

CplexA is a Mathematica package that efficiently computes probabilities and properties of macromolecular assemblies involved in gene regulation, overcoming exponential complexity in configurational states.

Contribution

It introduces a novel computational approach using functional programming to analyze complex gene regulatory assemblies.

Findings

Enables analysis of gene expression regulation involving multiple DNA binding sites.

Efficiently handles exponential growth of configurational states.

Provides a freely available tool for researchers in molecular biology.

Abstract

Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions. The package is particularly suited to study gene expression at complex promoters controlled by multiple, local and distal, DNA binding sites for transcription factors. Availability: CplexA is freely available together with documentation at http://sourceforge.net/projects/cplexa/.