Protein

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

3 monthes ago   |   By Springer

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...
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