Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors

DOI10.1016/j.jcp.2010.02.009zbMath1214.68477OpenAlexW2118874283MaRDI QIDQ974299

Stephen Poole, Ali Khajeh-Saeed, J. Blair Perot

Publication date: 27 May 2010

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcp.2010.02.009

zbMATH Keywords

GPUsequence matchinggraphics processorparallel scanSmith-Waterman

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08) Algorithms on strings (68W32)

Related Items (3)

A PARALLEL ALGORITHM FOR THE CONSTRAINED MULTIPLE SEQUENCE ALIGNMENT PROBLEM DESIGNED FOR GPUs ⋮ PARALLEL 3D FINITE-DIFFERENCE TIME-DOMAIN METHOD ON MULTI-GPU SYSTEMS ⋮ GPU accelerated simulations of 3D deterministic particle transport using discrete ordinates method

Uses Software

• CUDA

Cites Work

• Algorithms on Strings, Trees and Sequences

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