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doi:10.1016/j.compbiolchem.2005.09.007 
Copyright © 2005 Elsevier Ltd All rights reserved.
Multilocus consensus genetic maps (MCGM): Formulation, algorithms, and results
Received 20 September 2005;
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Abstract
In process of creating genetic maps different labs/research groups obtain overlapping parts of the map. Merging these parts into one integrative map is based on looking for maximum shared marker orders among the maps. Really, not all shared markers of such maps have consensus order that obstructs building of the integrative maps. In this paper we propose a new approach to build verified multilocus consensus genetic maps in which shared markers always are integrated in stable consensus order. The approach is based on combined analysis of initial mapping data rather than manipulating with previously constructed maps. We show that more effective and reliable solutions may be obtained based on “synchronized ordering” facilitated by cycles of “re-sampling → ordering → removing unstable markers”. The proposed formulation of consensus genetic mapping can be considered as a version of traveling salesperson problem (TSP) that we refer to as synchronized-TSP. From the viewpoint of optimization, synchronized-TSP belongs to discrete constrained optimization problems. Earlier we developed new powerful and fast guided evolution strategy algorithms for some types of discrete constrained optimization. These algorithms were used here as a basis for solving more challenging problems of consensual marker ordering.
Keywords: Multilocus ordering; TSP; Synchronized discrete optimization; Re-sampling verification; Unstable neighborhoods
Article Outline
- 1. Introduction
- 2. MCGM problems: mathematical models and algorithms
- 2.1. Consensus order formulation
- 2.2. The essence and particularities of the approach
- 2.3. Choosing optimization algorithm for synchronized TSP
- 2.4. The algorithm for consensus map constructing
- 3. Results and discussion
- 3.1. Gender-dependent recombination distance matrixes (MCGM, case B)
- 3.2. Multilocus ordering with data from different mapping populations (MCGM, case C)
- 4. Concluding remarks
- Acknowledgements
- Appendix A. Appendix: Algorithm of searching for all consensual orders
- References
