Comparison between simulated annealing algorithms and rapid chain delineation in the construction of genetic maps

Genetics and Molecular Biology

Moysés Nascimento²  Cosme Damião Cruz¹  Luiz Alexandre Peternelli²  Ana Carolina Mota Campana² 

[1] ,Universidade Federal de Viçosa Departamento de Estatística

关键词: better order;    genetic mapping;    genomic analyses;    stochastic optimization;   

DOI  :  10.1590/S1415-47572010005000033

来源: SciELO

【 摘 要 】

The efficiency of simulated annealing algorithms and rapid chain delineation in establishing the best linkage order, when constructing genetic maps, was evaluated. Linkage refers to the phenomenon by which two or more genes, or even more molecular markers, can be present in the same chromosome or linkage group. In order to evaluate the capacity of algorithms, four F2 co-dominant populations, 50, 100, 200 and 1000 in size, were simulated. For each population, a genome with four linkage groups (100 cM) was generated. The linkage groups possessed 51, 21, 11 and 6 marks, respectively, and a corresponding distance of 2, 5, 10 and 20 cM between adjacent marks, thereby causing various degrees of saturation. For very saturated groups, with an adjacent distance between marks of 2 cM and in greater number, i.e., 51, the method based upon stochastic simulation by simulated annealing presented orders with distances equivalent to or lower than rapid chain delineation. Otherwise, the two methods were commensurate through presenting the same SARF distance.

【 授权许可】

CC BY   
 All the contents of this journal, except where otherwise noted, is licensed under a Creative Commons Attribution License