Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences-Reference-Cited by-同舟云学术

Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences

Published:2015-10-06 Issue:1 Volume:16 Page:
ISSN:1471-2105
Container-title:BMC Bioinformatics
language:en
Short-container-title:BMC Bioinformatics

Author:

Okada Daiki,Ino Fumihiko,Hagihara Kenichi

Funder

Japan Society for the Promotion of Science

Publisher

Springer Science and Business Media LLC

Subject

Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology

Link

http://link.springer.com/content/pdf/10.1186/s12859-015-0744-4.pdf

Reference34 articles.

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3. de O. Sandes EF, de Melo ACMA. CUDAlign: Using GPU to accelerate the comparison of megabase genomic sequences. In: Proc. 15th ACM SIGPLAN Symp. Principles and Practice of Parallel Programming (PPoPP’10). ACM: 2010. p. 137–46.

4. Blazewicz J, Frohmberg W, Kierzynka M, Pesch E, Wojciechowski P. Protein alignment algorithms with an efficient backtracking routine on multiple GPUs. BMC Bioinforma. 2011; 12(181):17.

5. Korpar M, Šikić M. Sw#–gpu-enabled exact alignments on genome scale. Bioinformatics. 2013; 29(19):2494–5.

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