Ridge regression based hybrid genetic algorithms for multi-locus quantitative trait mapping
International Journal of Bioinformatics Research and Applications
Performance Modeling and Analysis of a Massively Parallel Direct - Part 1
International Journal of High Performance Computing Applications
Algorithm 897: VTDIRECT95: Serial and parallel codes for the global optimization algorithm direct
ACM Transactions on Mathematical Software (TOMS)
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
A power aware study for VTDIRECT95 using DVFS
SpringSim '09 Proceedings of the 2009 Spring Simulation Multiconference
Research article: Assessing a multiple QTL search using the variance component model
Computational Biology and Chemistry
Using parallel computing and grid systems for genetic mapping of quantitative traits
PARA'06 Proceedings of the 8th international conference on Applied parallel computing: state of the art in scientific computing
| Hi-index | 3.84 |
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