Improved prediction of bacterial transcription start sites
(2006) Improved prediction of bacterial transcription start sites. Bioinformatics 22(2):pp. 142-148.
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Abstract
Motivation: Identifying bacterial promoters is an important step toward understanding gene regulation. In this paper, we address the problem of predicting the location of promoters and their transcription start sites (TSSs) in Escherichia coli. The accepted method for this problem is to use position weight matrices (PWMs), which define conserved motifs at the sigma-factor binding site. However this method is known to result in a large numbers of false positive predictions. Results: Our approaches to TSS prediction are based upon an ensemble of support vector machines (SVMs) employing a variant of the mismatch string kernel. This classifier is sub-sequently combined with a PWM and a model based on distribution of distances from TSS to gene start. We investi-gate the effect of different scoring techniques and quantify performance using area under a detection-error tradeoff curve. When tested on a biologically realistic task, our method provides performance comparable or superior to the best reported for this task. False positives are significantly reduced, an improvement of great significance to biologists.
| Item Type: | Journal Article |
|---|---|
| RM Number: | 2007000446 |
| Status: | Published |
| Keywords: | bacterial promoters, support vector machines |
| 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: | 7549 |
| Deposited By: | Towsey, Michael W. |
| Deposited On: | 14 May 2007 |
| Alternative Locations: | http://dx.doi.org/10.1093/bioinformatics/bti771 |
| Copyright Owner: | Copyright 2006 (The authors): Licensed to Oxford University Press |
| Additional Information: | For more information, please refer to the journal’s website (see link) or contact the author. Author contact details: m.towsey@qut.edu.au |