Simultaneous search for multiple QTL using the global optimization algorithm DIRECT.
BACKGROUND
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.


BACKGROUND
The code of the prototype implementation is available at http://user.it.uu.se/~kl/qtl_software.html
Ljungberg
K
K
Information Technology, Division of Scientific Computing, Uppsala University, P.O. Box 337,751 05 Uppsala, Sweden. Kajsa.Ljungberg@it.uu.se
Holmgren
S
S
Carlborg
O
O
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D040641:Quantitative Trait Loci / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software