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Genome Data Analysis Using MapReduce Paradigm
(Institute of Electrical and Electronics Engineers Inc., 2015) Pahadia, M.; Srivastava, A.; Srivastava, D.; Patil, N.
Counting the number of occurences of a substringin a string is a problem in many applications. This paper suggests a fast and efficient solution for the field of bioinformatics. Ak-mer is a k-length sub string of a biological sequence. K-mercounting is defined as counting the number of occurences of all the possible k-mers in a biological sequence. K-mer counting has uses in applications ranging from error correction of sequencing reads, genome assembly, disease prediction and feature extraction. The current k-mer counting tools are both time and space costly. We provide a solution which uses MapReduce and Hadoop to reduce the time complexity. After applying the algorithms on real genome datasets, we concluded that the algorithm using Hadoopand MapReduce Paradigm runs more efficiently and reduces the time complexity significantly. Â© 2015 IEEE.