Enter Your Search:
Results 1-3 (3)
Go to page number:
Select a Filter Below
Advances and Applications in Bioinformatics and Chemistry : AABC (1)
G3: Genes|Genomes|Genetics (1)
Journal of Computational Biology (1)
Holmgren, Sverker (3)
Nettelblad, Carl (2)
Besnier, Francois (1)
Carlborg, Örjan (1)
Crooks, Lucy (1)
Ek, Weronica (1)
Kierczak, Marcin (1)
Ljungberg, Kajsa (1)
Mahjani, Behrang (1)
Mishchenko, Kateryna (1)
Nelson, Ronald M. (1)
Pettersson, Mats E. (1)
Rönnegård, Lars (1)
Shen, Xia (1)
Sheng, Zheya (1)
Álvarez-Castro, José M. (1)
Year of Publication
Did you mean:
MAPfastR: Quantitative Trait Loci Mapping in Outbred Line Crosses
Nelson, Ronald M.
Pettersson, Mats E.
Álvarez-Castro, José M.
MAPfastR is a software package developed to analyze quantitative trait loci data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate quantitative trait loci analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7
QTL mapping; inbred line cross; outbred line cross; quantitative genetics
Fast and Accurate Detection of Multiple Quantitative Trait Loci
Journal of Computational Biology
We present a new computational scheme that enables efficient and reliable quantitative trait loci (QTL) scans for experimental populations. Using a standard brute-force exhaustive search effectively prohibits accurate QTL scans involving more than two loci to be performed in practice, at least if permutation testing is used to determine significance. Some more elaborate global optimization approaches, for example, DIRECT have been adopted earlier to QTL search problems. Dramatic speedups have been reported for high-dimensional scans. However, since a heuristic termination criterion must be used in these types of algorithms, the accuracy of the optimization process cannot be guaranteed. Indeed, earlier results show that a small bias in the significance thresholds is sometimes introduced.
Our new optimization scheme, PruneDIRECT, is based on an analysis leading to a computable (Lipschitz) bound on the slope of a transformed objective function. The bound is derived for both infinite- and finite-size populations. Introducing a Lipschitz bound in DIRECT leads to an algorithm related to classical Lipschitz optimization. Regions in the search space can be permanently excluded (pruned) during the optimization process. Heuristic termination criteria can thus be avoided. Hence, PruneDIRECT has a well-defined error bound and can in practice be guaranteed to be equivalent to a corresponding exhaustive search. We present simulation results that show that for simultaneous mapping of three QTLS using permutation testing, PruneDIRECT is typically more than 50 times faster than exhaustive search. The speedup is higher for stronger QTL. This could be used to quickly detect strong candidate eQTL networks.
algorithms; branch-and-bound; genetic mapping; genomics; statistical models; statistics
Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits
Advances and Applications in Bioinformatics and Chemistry : AABC
We present a two-phase strategy for optimizing a multidimensional, nonconvex function arising during genetic mapping of quantitative traits. Such traits are believed to be affected by multiple so called quantitative trait loci (QTL), and searching for d QTL results in a d-dimensional optimization problem with a large number of local optima. We combine the global algorithm DIRECT with a number of local optimization methods that accelerate the final convergence, and adapt the algorithms to problem-specific features. We also improve the evaluation of the QTL mapping objective function to enable exploitation of the smoothness properties of the optimization landscape. Our best two-phase method is demonstrated to be accurate in at least six dimensions and up to ten times faster than currently used QTL mapping algorithms.
global optimization; QTL mapping; DIRECT
Results 1-3 (3)
Go to page number:
Remove citation from clipboard
Add citation to clipboard
This will clear all selections from your clipboard. Do you wish proceed?
Clipboard is full! Please remove an item and try again.
PubMed Central Canada is a service of the
Canadian Institutes of Health Research
(CIHR) working in partnership with the National Research Council's
national science library
in cooperation with the
National Center for Biotechnology Information
U.S. National Library of Medicine
(NCBI/NLM). It includes content provided to the
PubMed Central International archive
by participating publishers.