The review of the acceleration of Smith-Waterman algorithm by using CUDA-enable GPU
- https://doi.org/10.2991/icmmita-15.2015.139How to use a DOI?
- Acceleration; Sequence alignment; Smith-Waterman algorithm; CUDA.
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.
- © 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/).
Cite this article
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 - https://doi.org/10.2991/icmmita-15.2015.139 ID - Jing2015/11 ER -