The review of the acceleration of Smith-Waterman algorithm by using CUDA-enable GPU

DOI

10.2991/icmmita-15.2015.139How to use a DOI?

Keywords

Acceleration; Sequence alignment; Smith-Waterman algorithm; CUDA.

Abstract

Smith-Waterman (SW) algorithm, which calculates the similarity between two given sequences, is broadly used in bioinformatics research field. However, the time complexity of the SW algorithm prevents it from being used for long sequence alignment. Since SW algorithm is based on dynamic programing, using single instruction multiple data parallel computing algorithm can significantly reduce the computing cost. For this reason, this review introduces three commonly used parallel computing algorithms based on Compute Unified Device Architecture (CUDA) for SW algorithm acceleration as well as illustrates their advantages and disadvantages.

Copyright

© 2015, the Authors. Published by Atlantis Press.

Open Access

This is an open access article distributed under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).

Download article (PDF)

TY  - CONF
AU  - Chenyang Jing
AU  - Le Zhang
PY  - 2015/11
DA  - 2015/11
TI  - The review of the acceleration of Smith-Waterman algorithm by using CUDA-enable GPU
BT  - Proceedings of the 2015 3rd International Conference on Machinery, Materials and Information Technology Applications
PB  - Atlantis Press
SP  - 734
EP  - 742
SN  - 2352-538X
UR  - https://doi.org/10.2991/icmmita-15.2015.139
DO  - 10.2991/icmmita-15.2015.139
ID  - Jing2015/11
ER  -