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

D. I. Mester, Y. I. Ronin, M. A. Korostishevsky, V. L. Pikus, A. E. Glazman, A. B. Korol

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)12-20
Number of pages9
JournalComputational Biology and Chemistry
Volume30
Issue number1
DOIs
StatePublished - Feb 2006

Bibliographical note

Funding Information:
The study was supported by the Israeli Ministry of Absorption.

Keywords

  • Multilocus ordering
  • Re-sampling verification
  • Synchronized discrete optimization
  • TSP
  • Unstable neighborhoods

ASJC Scopus subject areas

  • Computational Mathematics
  • Structural Biology
  • Biochemistry
  • Organic Chemistry

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