Paper Info
Title
Evolutionary algorithms for the selection of single nucleotide polymorphisms.
Abstract
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.
Year
DOI
Venue
2003
10.1186/1471-2105-4-30
BMC Bioinformatics
Keywords
Field
DocType
computer simulation,evolutionary algorithm,bioinformatics,computational biology,search space,genetic markers,single nucleotide polymorphism,optimization problem,genetic marker,major histocompatibility complex,microarrays,intellectual property,population study,programming languages,algorithms
Gene,Biology,Evolutionary algorithm,Tag SNP,Genomics,Single-nucleotide polymorphism,Bioinformatics,Genetics,Locus (genetics),SNP,Evolutionary biology,DNA microarray
Journal
Volume
Issue
ISSN
4
1
1471-2105
Citations 
PageRank 
References 
16
1.20
9
Authors
3
Name
Order
Citations
PageRank
Robert M. Hubley1342.65
Eckart Zitzler24678291.01
Jared C Roach3313.67