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Bioinformatics Advance Access published online on June 16, 2005
Bioinformatics, 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@oupjournals.org
Received May 2, 2005
Revised June 3, 2005
Accepted June 15, 2005

Applications note

DNA-BAR: distinguisher selection for DNA barcoding

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

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

* To whom correspondence should be addressed.
I. I. Mandoiu, E-mail: ion{at}cse.uconn.edu


  Abstract

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.


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