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Statler College of Engineering and Mining Resources


Lane Department of Computer Science and Electrical Engineering


Background: Alignment-free sequence similarity analysis methods often lead to significant savings in computational time over alignment-based counterparts.

Results: Anewalignment-freesequencesimilarityanalysismethod,calledSSAWisproposed.SSAWstandsfor Sequence Similarity Analysis using the Stationary Discrete Wavelet Transform (SDWT). It extracts k-mers from a sequence, then maps each k-mer to a complex number field. Then, the series of complex numbers formed are transformed into feature vectors using the stationary discrete wavelet transform. After these steps, the original sequence is turned into a feature vector with numeric values, which can then be used for clustering and/or classification.

Conclusions: Usingtwodifferenttypesofapplications,namely,clusteringandclassification,wecomparedSSAW against the the-state-of-the-art alignment free sequence analysis methods. SSAW demonstrates competitive or superior performance in terms of standard indicators, such as accuracy, F-score, precision, and recall. The running time was significantly better in most cases. These make SSAW a suitable method for sequence analysis, especially, given the rapidly increasing volumes of sequence data required by most modern applications.

Source Citation

Lin, J., Wei, J., Adjeroh, D., Jiang, B.-H., & Jiang, Y. (2018). SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform. BMC Bioinformatics, 19(1).


© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.



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