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GPU acceleration of Fitch’s parsimony on protein data: from Kepler to Turing

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Abstract

The analysis of complex biological datasets beyond DNA scenarios is gaining increasing interest in current bioinformatics. Particularly, protein sequence data introduce additional complexity layers that impose new challenges from a computational perspective. This work is aimed at investigating GPU solutions to address these issues in a representative algorithm from the phylogenetics field: Fitch’s parsimony. GPU strategies are adopted in accordance with the protein-based formulation of the problem, defining an optimized kernel that takes advantage of data parallelism at the calculations associated with different amino acids. In order to understand the relationship between problem sizes and GPU capabilities, an extensive evaluation on a wide range of GPUs is conducted, covering all the recent NVIDIA GPU architectures—from Kepler to Turing. Experimental results on five real-world datasets point out the benefits that imply the exploitation of state-of-the-art GPUs, representing a fitting approach to address the increasing hardness of protein sequence datasets.

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Acknowledgements

This work was partially funded by the AEI (State Research Agency, Spain) and the ERDF (European Regional Development Fund, EU), under the contract TIN2016-76259-P (PROTEIN Project), as well as Portuguese national funds through FCT (Fundação para a Ciência e a Tecnologia, Portugal) Projects UIDB/50021/2020 and LISBOA-01-0145-FEDER-031901 (PTDC/CCI-COM/31901/2017, HiPErBio). Sergio Santander-Jiménez is supported by the Post-Doctoral Fellowship from FCT under Grant SFRH/BPD/119220/2016.

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Santander-Jiménez, S., Vega-Rodríguez, M.A., Zahinos-Márquez, A. et al. GPU acceleration of Fitch’s parsimony on protein data: from Kepler to Turing. J Supercomput 76, 9827–9853 (2020). https://doi.org/10.1007/s11227-020-03225-x

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