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A fast and simple approach to k-mer decomposition
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Abstract
Alignment searches are fast heuristic methods to identify similar regions between two sequences. This group of algorithms is ubiquitously used in a myriad of software to find homologous sequences or to map sequence reads to genomes. Often the first step in alignment searches is k-mer decomposition: listing all overlapping subsequences of length k. This article presents a simple integer representation of k-mers and shows how a sequence can be quickly decomposed into k-mers in constant time with respect to k.
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