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Bioinformatics Advance Access originally published online on June 16, 2005
Bioinformatics 2005 21(16):3424-3426; doi:10.1093/bioinformatics/bti547
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

DNA-BAR: distinguisher selection for DNA barcoding

B. DasGupta 1,{dagger}, K. M. Konwar 2, I. I. Mandoiu 2,* and A. A. Shvartsman 2

1Department of Computer Science, University of Illinois at Chicago Chicago, IL 60607-7053, USA
2Computer Science and Engineering Department, University of Connecticut 371 Fairfield Road, Unit 2155, Storrs, CT 06269-2155, USA

*To whom correspondence should be addressed.

Summary: DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.

Availability: DNA-BAR can be used online through the web interface provided at http://dna.engr.uconn.edu/~software/DNA-BAR/. The open source C code, released under the GNU General Public License, is also available at the above address.

Contact:ion{at}engr.uconn.edu

Received on May 2, 2005; revised on June 3, 2005; accepted on June 15, 2005

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