Conference Paper

Large-Scale DNA Sequence Assembly by Using Computing Grid

DOI: 10.1109/GCCW.2006.59 Conference: Grid and Cooperative Computing Workshops - GCC 2006, 5th International Conference, Changsha, Hunan, China, 21-23 October 2006, Proceedings
Source: DBLP


DNA sequence assembly is a fundamental part of biological computing. However, most of the large-scale sequence assemblies require intensive computing power and huge storage. To speed up the assembly process, we here propose a method for large-scale DNA sequence assembly by using computing grid. The central idea of our method is to first cluster the input of fragment set into many non-intersected subsets using k-mers and then to distribute them to all nodes of the grid-computing system. Our method has accuracy of more than 92% on the test data sets under the simulated grid-computing system but costing shorter time and lower storage. Our method can efficiently process large-scale DNA sequence assembly by taking advantage of huge storage and computing capacity of computing gird

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    ABSTRACT: The aim of this paper is to illustrate the automatic test generation for combinational circuits based on DNA computing. In the algorithm the chromosomes are encoded by the four bases of nucleic acid Sigma = {A,G,C,T} and the gene-class genetic manipulation is introduced to ensure the population diversity; In addition, the test set size produced by DNA chain is controlled at different stages of test generation so as to reduce the redundancy of test sets and accelerate the speed of test generation. The experimental results for benchmark circuit iscas'85 show that this algorithm can achieve high fault coverage and substantially reduce the size of test vector sets.
    No preview · Article · Aug 2009