Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.
Optimal robust non-unique probe selection using Integer Linear Programming
1 Institute of Computer Graphics and Algorithms, Vienna University of Technology, Favoritenstraße 9-11, 1040 Vienna, Austria, 2 Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 73, D-14195 Berlin, Germany and 3 Algorithmic Bioinformatics, Free University Berlin, Takustraße 9, 14195 Berlin, Germany
Received on January 15, 2004; accepted on March 1, 2004
Motivation: Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the presence or absence of biological agents, the targets, in a sample. Given a collection of genetic sequences of targets one faces the challenge of finding short oligonucleotides, the probes, which allow detection of targets in a sample. Each hybridization experiment determines whether the probe binds to its corresponding sequence in the target. Depending on the problem, the experiments are conducted using either unique or non-unique probes and usually assume that only one target is present in the sample. The problem at hand is to compute a design, i.e. a minimal set of probes that allows to infer the targets in the sample from the result of the hybridization experiment. If we allow to test for more than one target in the sample, the design of the probe set becomes difficult in the case of non-unique probes.
Results: Building upon previous work on group testing for microarrays, we describe the first approach to select a minimal probe set for the case of non-unique probes in the presence of a small number of multiple targets in the sample. The approach is based on an ILP formulation and a branch-and-cut algorithm. Our preliminary implementation greatly reduces the number of probes needed while preserving the decoding capabilities.
Availability: http://www.inf.fu-berlin.de/inst/ag-bio
Contact: reinert{at}inf.fu-berlin.de
* To whom correspondence should be addressed.
Present address: Genome Informatics, Faculty of Technology, University of Bielefeld, D-33595 Bielefeld, Germany.
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