Abstract
Genome subsequence assembly plays an important role in personalized medicine and genome variation. Third generation sequencing mechanisms were very crucial problems of subsequence assembly. For example mapping the subsequences or finding the identical positions in them is one of the rigid challenges in Bioinformatics. In this paper, we introduce a novel methodology of MapReduce Maximum Exact Matches (MR-MEM) which effectively utilizes the MapReduce program while finding and mapping between genome subsequences using parallel suffix and prefix index structure. The proposed technique works by aligning fragments according to the reference genome. A fragment subsequence is initially matched with the genome to identify the probable matching locations. These identified locations are then analyzed for complete matches. We find the best matching fragment that is assigned to the location by finding the hamming distance between the query sequence and genome reference. The implementation results show that the proposed approach exhibits faster and accurate alignments by providing very low gaps and very high exact alignments.
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