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Bioinformatics Advance Access published online on September 16, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn494
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

tCal: transcriptional probability calculator using thermodynamic model

Xin Zhou 1 and Zhen Su 1,*

1College of Biological Sciences, China Agricultural University.

*To whom correspondence should be addressed. Su Zhen, E-mail: zhensu{at}cau.edu.cn


  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, "tCal". 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.

Availability: tCal module and its online version can be found at: http://bioinformatics.cau.edu.cn/tCal.

Contact: zhensu{at}cau.edu.cn

Associate Editor: Prof. John Quackenbush

Received on July 2, 2008; revised on August 27, 2008; accepted on September 12, 2008

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