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A Study on Ordering Molecular Marker Loci in a Genetic Linkage Group

Author: DongChengLing
Tutor: TongChunFa
School: Nanjing Forestry University
Course: Applied Computer Technology
Keywords: Genetic linkage map Simulated annealing algorithm Heuristic search algorithm Hidden Markov model (HMM) Message Passing Interface (MPI)
CLC: TP18
Type: Master's thesis
Year: 2011
Downloads: 22
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Abstract


The genetic linkage map is a very important field of genetic breeding studies , linkage map construction work include : two-point linkage analysis , multi-locus linkage analysis , linkage group divided into a number of points such as sorting . The genetic linkage map of the key issues is to determine the marker locus on the chromosome position and its linear arrangement , which involves a number of points sorted the problem . Exhaustive method is feasible for a small amount of marker loci moderate number of marker loci in linkage group is concerned , however , it is all possible sort is very huge . The multilocus sort are famous to find the optimal solution of NP problems or called TSP problem . Solving methods either is not high on the accuracy of the optimal solution , either requires a lot of computer resources . Multilocus linkage analysis method based on hidden Markov model (HMM) , verified by computer simulation of the maximum likelihood value as the objective function in the the multilocus sort of validity , and summarizes the different computing environments required the calculation time . Linkage groups contain more marker loci multilocus simulated annealing parallel heuristic search algorithms and multilocus parallel algorithms , and programming with C MPI way . Confirmed by computer simulation of a large number of parallel algorithm is fast and efficient , with higher accuracy than the the famous mapping software Mapmaker to F2 on behalf of mapping population . The results of this paper can help build a forest of high-density genetic linkage map .

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