tCal: Transcriptional probability calculator using thermodynamic model

Abstract

Summary: Thermodynamic model has been proposed as a realistic model of gene transcriptional regulation in bacteria, in which transcription probability calculation is based on physical interpretation of biological knowledge. We extend the published results in this area, and derive a relatively new model which could serve as a generalized form of previous results. To facilitate the application in gene network modeling studies, we implement our model in a Python module, 'Cal'. With minimum programming efforts, user can use tCal to build transcription units, and either compute the transcription probabilities, or construct SBML models of regulatory networks. © The Author 2008. Published by Oxford University Press. All rights reserved.