Tomas Farkas, Jozef Sitarcik, Brona Brejova, Maria Lucka. SWSPM: A Novel Alignment-Free DNA Comparison Method Based on Signal ProcessingApproaches. Evolutionary Bioinformatics, 15:1176934319849071. 2019.

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Computing similarity between 2 nucleotide sequences is one of the fundamental
problems in bioinformatics. Current methods are based mainly on 2 major
approaches: (1) sequence alignment, which is computationally expensive, and (2)
faster, but less accurate, alignment-free methods based on various statistical
summaries, for example, short word counts. We propose a new distance measure
based on mathematical transforms from the domain of signal processing. To
tolerate large-scale rearrangements in the sequences, the transform is computed
across sliding windows. We compare our method on several data sets with current
state-of-art alignment-free methods. Our method compares favorably in terms of
accuracy and outperforms other methods in running time and memory requirements.
In addition, it is massively scalable up to dozens of processing units without
the loss of performance due to communication overhead. Source files and sample
data are available at