K Ljungberg1, S Holmgren, O Carlborg. 1. Information Technology, Division of Scientific Computing, Uppsala University, P.O. Box 337,751 05 Uppsala, Sweden. Kajsa.Ljungberg@it.uu.se
Abstract
MOTIVATION: 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. RESULTS: 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. AVAILABILITY: The code of the prototype implementation is available at http://user.it.uu.se/~kl/qtl_software.html
MOTIVATION: 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. RESULTS: 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. AVAILABILITY: The code of the prototype implementation is available at http://user.it.uu.se/~kl/qtl_software.html