Abstract
Modern graphical processing units (GPUs) offer much more computational power than modern CPUs, so it is natural that GPUs are often used for solving many computationally-intensive problems. One of the tasks of huge importance in bioinformatics is sequence alignment. We investigate its variant introduced a few years ago in which some additional requirement on the alignment is given. As a result we propose a parallel version of Center-Star algorithm computing the constrained multiple sequence alignment at the GPU. The obtained speedup over the serial CPU relative is in range [20, 200].
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Gudyś, A., Deorowicz, S. (2011). A Parallel GPU-Designed Algorithm for the Constrained Multiple Sequence Alignment Problem. In: Czachórski, T., Kozielski, S., Stańczyk, U. (eds) Man-Machine Interactions 2. Advances in Intelligent and Soft Computing, vol 103. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23169-8_39
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DOI: https://doi.org/10.1007/978-3-642-23169-8_39
Publisher Name: Springer, Berlin, Heidelberg
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