A new approach to the non-unique probe selection problem

Identification of biological agents in a sample is a relevant problem in medicine. A model to this problem consists of selecting optimal oligonucleotide probe sets for use in hybridization experiments in which target viruses or bacteria are to be identified in biological samples. In such an experime...

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Bibliographic Details
Published in:Annals of biomedical engineering 2007-04, Vol.35 (4), p.651-658
Main Authors: Meneses, Cláudio N, Pardalos, Panos M, Ragle, Michelle A
Format: Article
Language:English
Subjects:
Algorithms
Bacteria
Biological
Biological properties
Biological samples
C++ based development systems
Computer Simulation
DNA Probes - chemistry
DNA Probes - genetics
DNA, Bacterial - analysis
DNA, Bacterial - chemistry
DNA, Bacterial - genetics
DNA, Viral - analysis
DNA, Viral - chemistry
DNA, Viral - genetics
Graphical user interface
Heuristic
Heuristic methods
Hybridization
Mathematical models
Models, Chemical
Nucleic Acid Hybridization
Oligonucleotides
Optimization
Probes
Software
Studies
Target recognition
Viruses
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Summary:Identification of biological agents in a sample is a relevant problem in medicine. A model to this problem consists of selecting optimal oligonucleotide probe sets for use in hybridization experiments in which target viruses or bacteria are to be identified in biological samples. In such an experiment the presence or absence of these targets is determined by observing whether selected probes bind to their corresponding sequences. The problem is to select a probe set that is able to uniquely identify targets while containing a minimal number of probes. In this paper we describe a heuristic algorithm that produced feasible solution sets that for large, real data sets contain significantly fewer probes than those obtained using other methods. A description of the problem, our approach, and the results are presented. We developed a C++ program and a GUI (Graphical User Interface) to run real and simulated instances of the problem.
ISSN:0090-6964
1573-9686
DOI:10.1007/s10439-006-9242-1