A Phylogenetic Approach to Genetic Map Refinement
Following various genetic mapping techniques conducted on different segregating populations, one or more genetic maps are obtained for a given species. However, recombination analyses and other methods for gene mapping often fail to resolve the ordering of some pairs of neighboring markers, thereby leading to sets of markers ambiguously mapped to the same position. Each individual map is thus a partial order defined on the set of markers, and can be represented as a Directed Acyclic Graph (DAG). In this paper, given a phylogenetic tree with a set of DAGs labeling each leaf (species), the goal is to infer, at each leaf, a single combined DAG that is as resolved as possible, considering the complementary information provided by individual maps, and the phylogenetic information provided by the species tree. After combining the individual maps of a leaf into a single DAG, we order incomparable markers by using two successive heuristics for minimizing two distances on the species tree: the breakpoint distance, and the Kemeny distance. We apply our algorithms to the plant species represented in the Gramene database, and we evaluate the simplified maps we obtained.
KeywordsDirected Acyclic Graph Total Order Phylogenetic Information Phylogenetic Approach Strongly Connect Component
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- 6.Jackson, B.N., Aluru, S., Schnable, P.S.: Consensus genetic maps: a graph theoretic approach. In: IEEE Computational Systems Bioinformatics Conference (CSB 2005), pp. 35–43 (2005)Google Scholar
- 10.Kemeny, J.P.: Mathematics without numbers. Daedelus 88, 577–591 (1959)Google Scholar
- 13.Pe’er, I., Shamir, R.: The median problems for breakpoints are NP-complete. In: Electronic Colloquium on Computational Complexity (ECCC), Report 71 (1998)Google Scholar
- 14.Saari, D., Merlin, V.: A geometric examination of Kemeny’s rule. Social Choice and Welfare 7, 81–90 (2000)Google Scholar
- 18.Yap, I.V., Schneider, D., Kleinberg, J., Matthews, D., Cartinhour, S., McCouch, S.R.: A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps. Genetics 165, 2235–2247 (2003)Google Scholar