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Multilocus consensus genetic maps (MCGM): Formulation, algorithms, and results

Paper ID Volume ID Publish Year Pages File Format Full-Text
15410 1411 2006 9 PDF Available
Title
Multilocus consensus genetic maps (MCGM): Formulation, algorithms, and results
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
First Page Preview
Multilocus consensus genetic maps (MCGM): Formulation, algorithms, and results
Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 30, Issue 1, February 2006, Pages 12–20
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering