Ljungberg K, Holmgren S, Carlborg O
Information Technology, Division of Scientific Computing, Uppsala University, P.O. Box 337,751 05 Uppsala, Sweden.
Bioinformatics. 2004 Aug 12;20(12):1887-95. doi: 10.1093/bioinformatics/bth175. Epub 2004 Mar 25.
A simultaneous search is necessary for maximizing the power to detect epistatic quantitative trait loci (QTL). The computational complexity demands that the traditional exhaustive search be replaced by a more efficient global optimization algorithm.
We have the previously known algorithm adapted DIRECT, to the problem of simultaneous mapping of multiple QTL. We have compared DIRECT with standard exhaustive search and a genetic algorithm previously used for QTL mapping in two dimensions. In all two- and three-QTL test cases, DIRECT accurately finds the global optimum two to four orders of magnitude faster than when using an exhaustive search, and one order of magnitude faster than when using the genetic algorithm. Thus, randomization testing for determining empirical significance thresholds for at least three QTL is made feasible by the use of DIRECT.
The code of the prototype implementation is available at http://user.it.uu.se/~kl/qtl_software.html
为了最大限度地提高检测上位性数量性状基因座（QTL）的能力，需要进行同步搜索。计算复杂性要求用更高效的全局优化算法取代传统的穷举搜索。
我们将先前已知的DIRECT算法应用于多个QTL的同步映射问题。我们将DIRECT与标准穷举搜索以及先前用于二维QTL映射的遗传算法进行了比较。在所有双QTL和三QTL测试案例中，DIRECT找到全局最优解的速度比使用穷举搜索快两到四个数量级，比使用遗传算法快一个数量级。因此，使用DIRECT使得确定至少三个QTL的经验显著性阈值的随机化测试变得可行。
