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| A Parallel Algorithm for Detecting Complexes in Protein-protein Interaction Networks with MapReduce |
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Abstract Detecting protein complexes from Protein-protein Interaction (PPI)
networks has been the focus of many recent efforts on protein. With
the appearance of big data and large scale PPI networks, traditional
sequential methods, which analyze interaction networks and detect
protein complexes, do not utilize high performance computing. In
this paper, we propose a parallel algorithm using cloud computing
method to improve the computational efficiency and detect protein
complexes. Because MapReduce programming model simplifies the
implementation of many data parallel applications, firstly we use it
to calculate the value of each edge and the value of each node from
PPI networks, then expand complexes. At last, we perform the
algorithm on different data to test the speedup of the algorithm.
Moreover, through the parallel algorithm is compared with sequential
method, experimental results show that the running time of parallel
algorithm is short. We get a conclusion that parallel algorithm can
also accurately assign proteins with similar functions to a complex.
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| Cite this article: |
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Zhenmei Yu,Zhangxu Li. A Parallel Algorithm for Detecting Complexes in Protein-protein Interaction Networks with MapReduce[J]. Journal of Fiber Bioengineering and Informatics, 2015, 8(3): 565-574.
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2015, Vol. 8 
