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Bioinformatics Advance Access originally published online on January 3, 2007
Bioinformatics 2007 23(4):487-492; doi:10.1093/bioinformatics/btl626
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Oligonucleotide microarray identification of Bacillus anthracis strains using support vector machines

M. Doran 1,*, D. S. Raicu 1, J. D. Furst 1, R. Settimi 1, M. Schipma 2 and D. P. Chandler 2,{dagger}

1 Intelligent Multimedia Processing Laboratory, School of Computer Science, Telecommunications and Information Systems, DePaul University Chicago, USA
2 Biodetection Technologies, Argonne National Laboratory Chicago, USA

*To whom correspondence should be addressed.


  Abstract

The capability of a custom microarray to discriminate between closely related DNA samples is demonstrated using a set of Bacillus anthracis strains. The microarray was developed as a universal fingerprint device consisting of 390 genome-independent 9mer probes. The genomes of B.anthracis strains are monomorphic and therefore, typically difficult to distinguish using conventional molecular biology tools or microarray data clustering techniques. Using support vector machines (SVMs) as a supervised learning technique, we show that a low-density fingerprint microarray contains enough information to discriminate between B.anthracis strains with 90% sensitivity using a reference library constructed from six replicate arrays and three replicates for new isolates.

Contact: doran_michael{at}msn.com

{dagger}Present address: Akonni Biosystems, Inc., Frederick, MD, USA

Associate Editor: Martin Bishop

Received on October 1, 2006; revised on November 30, 2006; accepted on December 4, 2006

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