Finding simple sequence repeats (SSRs) within human genome using MapReduce based K-mer algorithm

摘要

Simple sequence repeats (SSRs) is a collection of the different short and repetitive oligonucleotides sequence that is primarily observed in between any large DNA sequence. In comparison to the standard DNA sequence, these short oligonucleotides may have distinct functions and structural properties. In this article, we have presented a massive parallel processing model for basic operations with k-mers from DNA sequences, based on SSRs function. We introduce a novel approach that finds SSRs using k-mer in the first step. We implement the MapReduce based K-mer algorithm for the advantage of parallel execution, which also enables the analysis of large datasets using of the distributed platform. We have compared the result with KAnalyze, a pipelined K-mer toolkit for finding different sizes of k-mer, and found significant improvement in terms of computational time. Our study shows that MapReduce based k-mer has the potential which reduces memory footprint and accurately identifies every SSR of any specified length. Our proposed MapReduce based k-mer method is useful for finding any Simple sequence repeats (SSRs) in large DNA sequences on any distributed platform.