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| Gene Read Mapping Algorithms Based on MapReduce |
| TU Jin-Jin,YANG Ming,GUO Li-Na |
| School of Computer Science and Technology,Nanjing Normal University,Nanjing 210046 |
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Abstract Massive data generated by the rapid development of RNA-seq sequencing technology make serious challenges to the original read mapping algorithm in the efficiency. A spaced seed indexing algorithm without considering splice site based on MapReduce(PSeqMap),a spaced seed indexingalgorithm considering splice site(PJuncSeqMap),and a load-balancing solution are proposed. The MapReduce framework is employed to parallelize spaced seed indexing algorithms. The experimental results on the Arabidopsis gene datasets show that the proposed algorithms take full advantage of storage and computing power of the clusters and process massive genetic data efficiently.
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Received: 05 June 2013
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2014, Vol. 27 
