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The cross-species prediction of bacterial promoters using a support vector machine

Paper ID Volume ID Publish Year Pages File Format Full-Text
15478 1416 2008 8 PDF Available
Title
The cross-species prediction of bacterial promoters using a support vector machine
Abstract

Due to degeneracy of the observed binding sites, the in silico prediction of bacterial σ70-like promoters remains a challenging problem. A large number of σ70-like promoters has been biologically identified in only two species, Escherichia coli and Bacillus subtilis. In this paper we investigate the issues that arise when searching for promoters in other species using an ensemble of SVM classifiers trained on E. coli promoters. DNA sequences are represented using a tagged mismatch string kernel. The major benefit of our approach is that it does not require a prior definition of the typical −35 and −10 hexamers. This gives the SVM classifiers the freedom to discover other features relevant to the prediction of promoters. We use our approach to predict σA promoters in B. subtilis and σ66 promoters in Chlamydia trachomatis. We extended the analysis to identify specific regulatory features of gene sets in C. trachomatis having different expression profiles. We found a strong −35 hexamer and TGN/−10 associated with a set of early expressed genes. Our analysis highlights the advantage of using TSS-PREDICT as a starting point for predicting promoters in species where few are known.

Keywords
TSS, transcript start site; SVM, support vector machine; PWM, position weight matrix; RBS, ribosomal binding site; GSS, gene start site; IC, information contentTranscript start site; σ70; Promoter; Support vector machine
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 32, Issue 5, October 2008, Pages 359–366
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us