@inproceedings{6ab8ee9900414b44a6b87febe95101fa,
title = "Fast and accurate similarity searching of biopolymer sequences with GPU and CUDA",
abstract = "CUDA is an architecture introduced by NVIDIA Corporation, which allows software developers to take advantage of GPU resources in order to increase the computational power. This paper presents an approach to accelerate the similarity searching of DNA and protein molecules through parallel alignments of their sequences with the use of GPU and CUDA. In order to optimally align two biopolymer sequences, such as amino acid or nucleotide sequences, we employ the Smith-Waterman algorithm. We present the optimization steps leading to achieve a very good efficiency of our implementation on GPU and we compare results of efficiency tests with other known implementations. The results show that it is possible to search bioinformatics databases accurately within a reasonable time.",
keywords = "CUDA, DNA, GPU, bioinformatics, parallel computing, proteins, sequence alignment",
author = "Robert Paw{\l}owski and Bozena Ma{\l}ysiak-Mrozek and Stanis{\l}aw Kozielski and Dariusz Mrozek",
year = "2011",
doi = "10.1007/978-3-642-24650-0\_20",
language = "English",
isbn = "9783642246494",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
number = "PART 1",
pages = "230--243",
booktitle = "Algorithms and Architectures for Parallel Processing - 11th International Conference, ICA3PP 2011, Proceedings",
edition = "PART 1",
note = "11th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2011 ; Conference date: 24-10-2011 Through 26-10-2011",
}