Evolutionary algorithms for the selection of single nucleotide polymorphisms
Hubley, Robert M.
Roach, Jared C.
- Journal Article
Rights / licenseIn Copyright - Non-Commercial Use Permitted
Background Large databases of single nucleotide polymorphisms (SNPs) are available for use in genomics studies. Typically, investigators must choose a subset of SNPs from these databases to employ in their studies. The choice of subset is influenced by many factors, including estimated or known reliability of the SNP, biochemical factors, intellectual property, cost, and effectiveness of the subset for mapping genes or identifying disease loci. We present an evolutionary algorithm for multiobjective SNP selection. Results We implemented a modified version of the Strength-Pareto Evolutionary Algorithm (SPEA2) in Java. Our implementation, Multiobjective Analyzer for Genetic Marker Acquisition (MAGMA), approximates the set of optimal trade-off solutions for large problems in minutes. This set is very useful for the design of large studies, including those oriented towards disease identification, genetic mapping, population studies, and haplotype-block elucidation. Conclusion Evolutionary algorithms are particularly suited for optimization problems that involve multiple objectives and a complex search space on which exact methods such as exhaustive enumeration cannot be applied. They provide flexibility with respect to the problem formulation if a problem description evolves or changes. Results are produced as a trade-off front, allowing the user to make informed decisions when prioritizing factors. MAGMA is open source and available at http://snp-magma.sourceforge.net. Evolutionary algorithms are well suited for many other applications in genomics Show more
Journal / seriesBMC Bioinformatics
Pages / Article No.
SubjectPOLYMORPHISMUS DER BIOMOLEKÜLE; NUKLEOTIDE + NUKLEOSIDPHOSPHATE (BIOCHEMIE); MOLEKULARE EVOLUTION (BIOLOGISCHE EVOLUTION); POLYMORPHISM OF BIOMOLECULES; NUCLEOTIDES + NUCLEOSIDE PHOSPHATES (BIOCHEMISTRY); MOLECULAR EVOLUTION (BIOLOGICAL EVOLUTION); Objective Function; Single Nucleotide Polymorphism; Evolutionary Algorithm; Haplotype Block; Single Nucleotide Polymorphism Location
Organisational unit02640 - Inst. f. Technische Informatik und Komm. / Computer Eng. and Networks Lab.
03429 - Thiele, Lothar / Thiele, Lothar
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