Bacterial promoter modelling and prediction for E. coli and B. subtilis with Beagle

Maetschke, Stefan R. and Towsey, Michael W. and Hogan, James M. (2006) Bacterial promoter modelling and prediction for E. coli and B. subtilis with Beagle. In Proceedings Workshop on Intelligent Systems for Bioinformatics (WISB-2006) 73, pages pp. 9-13, Hobart, Tasmania.

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Abstract

We constructed sigma70-promoter models of varying complexity to predict promoter locations and to evaluate the importance of specific promoter elements. For this purpose, a novel software, named Beagle, was developed that utilizes an easy description language to conveniently specify promoter models. Model specifications are translated into position weight matrices and gap distributions which are refined using data from known promoters. The method is transparent, fast and allows the rapid exploration of different promoter models. Applied to promoter prediction in E. coli and B. subtilis, we show that inclusion of UP-elements and extended -10 motifs into the model yields a significant increase in prediction accuracy. The software, data sets and extended results can be downloaded at http://eresearch.fit.qut.edu.au/Beagle/.

Item Type:	Conference Paper
Status:	Published
Keywords:	Bacterial promoters, sigma factor, Escherichia coli, Bacillus subtilis
Subjects:	230000 Mathematical Sciences > 239900 Other Mathematical Sciences > 239901 Biological Mathematics 280000 Information, Computing and Communication Sciences > 280200 Artificial Intelligence and Signal and Image Processing > 280207 Pattern Recognition 280000 Information, Computing and Communication Sciences > 280200 Artificial Intelligence and Signal and Image Processing > 280213 Other Artificial Intelligence
ID Code:	7583
Deposited By:	Towsey, Michael W.
Deposited On:	14 May 2007
Alternative Locations:	http://portal.acm.org/citation.cfm?id=1274174
Copyright Owner:	Copyright 2006 Australian Computer Society
Copyright Statement:	Reproduced in accordance with the copyright policy of the publisher.