Mester D I, Ronin Y I, Hu Y, Peng J, Nevo E, Korol A B
Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 31905, Israel.
Theor Appl Genet. 2003 Oct;107(6):1102-12. doi: 10.1007/s00122-003-1305-1. Epub 2003 Aug 20.
The paper is devoted to the problem of multipoint gene ordering with a particular focus on "dominance" complication that acts differently in conditions of coupling-phase and repulsion-phase markers. To solve the problem we split the dataset into two complementary subsets each containing shared codominant markers and dominant markers in the coupling-phase only. Multilocus ordering in the proposed algorithm is based on pairwise recombination frequencies and using the well-known travelling salesman problem (TSP) formalization. To obtain accurate results, we developed a multiphase algorithm that includes synchronized-marker ordering of two subsets assisted by re-sampling-based map verification, combining the resulting maps into an integrated map followed by verification of the integrated map. A new synchronized Evolution-Strategy discrete optimization algorithm was developed here for the proposed multilocus ordering approach in which common codominant markers facilitate stabilization of the marker order of the two complementary maps. High performance of the employed algorithm allows systematic treatment for the problem of verification of the obtained multilocus orders, based on computing-intensive bootstrap and jackknife technologies for detection and removing unreliable marker scores. The efficiency of the proposed algorithm was demonstrated on simulated and real data.
本文致力于多点基因排序问题，特别关注“显性”并发症，该并发症在偶联相和排斥相标记条件下表现不同。为了解决该问题，我们将数据集拆分为两个互补子集，每个子集仅包含共享的共显性标记和偶联相中的显性标记。所提出算法中的多位点排序基于成对重组频率，并使用著名的旅行商问题（TSP）形式化。为了获得准确结果，我们开发了一种多阶段算法，该算法包括对两个子集进行同步标记排序，并通过基于重采样的图谱验证来辅助，将得到的图谱合并为一个综合图谱，然后对综合图谱进行验证。在此为所提出的多位点排序方法开发了一种新的同步进化策略离散优化算法，其中常见的共显性标记有助于稳定两个互补图谱的标记顺序。所采用算法的高性能允许基于计算密集型的自助法和刀切法技术对获得的多位点顺序进行验证，以检测和去除不可靠的标记分数。所提出算法的效率在模拟数据和真实数据上得到了证明。
