Bioinformatics Vol. 18 no. 10 2002
Pages 1340-1349
© 2002 Oxford University Press
Selecting signature oligonucleotides to identify organisms using DNA arrays
1 Center for Applied Computer Sciences Cologne (ZAIK),
University of Cologne, Weyertal 80, 50931 Köln, Germany
2 Department of Computational Molecular Biology,
MPI for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
Received on December 5, 2001
; revised on February 4, 2002
; accepted on March 27, 2002
Motivation: DNA arrays are a very useful tool to quickly identify biological agents present in some given sample, e.g. to identify viruses causing disease, for quality control in the food industry, or to determine bacteria contaminating drinking water. The selection of specific oligos to attach to the array surface is a relevant problem in the experiment design process. Given a set S of genomic sequences (the target sequences), the task is to find at least one oligonucleotide, called probe, for each sequence in S. This probe will be attached to the array surface, and must be chosen in a way that it will not hybridize to any other sequence but the intended target. Furthermore, all probes on the array must hybridize to their intended targets under the same reaction conditions, most importantly at the temperature T at which the experiment is conducted.
Results: We present an efficient algorithm for the probe design problem. Melting temperatures are calculated for all possible probe–target interactions using an extended nearest-neighbor model, allowing for both non-Watson–Crick base-pairing and unpaired bases within a duplex. To compute temperatures efficiently, a combination of suffix trees and dynamic programming based alignment algorithms is introduced. Additional filtering steps during preprocessing increase the speed of the computation.
The practicability of the algorithms is demonstrated by two
case studies: The identification of HIV-1 subtypes, and of 28S
rDNA sequences from 
400 organisms.
Availability: The software is available on request.
Contact: kaderali{at}zpr.uni-koeln.de
* To whom correspondence should be addressed.
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