Benchmarking of alignment-free sequence comparison methods

Zielezinski, A.; Girgis, H. Z.; Bernard, G.; Leimeister, C.-A.; Tang, K.; Dencker, T.; Lau, A. K.; Roehling, S.; Choi, J.; Waterman, M. S.; Comin, M.; Kim, S.-H.; Vinga, S.; Almeida, J. S.; Chan, C. X.; James, B.; Sun, F.; Morgenstern, B.; Karlowski, W. M.

doi:10.1101/611137

bioRxiv · 10.1101/611137

Benchmarking of alignment-free sequence comparison methods

Zielezinski, A.·Girgis, H. Z.·Bernard, G.·Leimeister, C.-A.·Tang, K.·Dencker, T.·Lau, A. K.·Roehling, S.·Choi, J.·Waterman, M. S.·Comin, M.·Kim, S.-H.·Vinga, S.·Almeida, J. S.·Chan, C. X.·James, B.·Sun, F.·Morgenstern, B.·Karlowski, W. M.

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Abstract

Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference and reconstruction of species trees under horizontal gene transfer and recombination events. The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.

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Zielezinski, A., Girgis, H. Z., Bernard, G., Leimeister, C.-A., Tang, K., Dencker, T., Lau, A. K., Roehling, S., Choi, J., Waterman, M. S., Comin, M., Kim, S.-H., Vinga, S., Almeida, J. S., Chan, C. X., James, B., Sun, F., Morgenstern, B., Karlowski, W. M.. 2019-04-16. Benchmarking of alignment-free sequence comparison methods. https://doi.org/10.1101/611137

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