Cargando…

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto t...

Descripción completa

Detalles Bibliográficos
Autores principales: Huang, Liang-Tsung, Wu, Chao-Chin, Lai, Lien-Fu, Li, Yun-Ju
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538332/
https://www.ncbi.nlm.nih.gov/pubmed/26339591
http://dx.doi.org/10.1155/2015/185179
_version_ 1782385988289429504
author Huang, Liang-Tsung
Wu, Chao-Chin
Lai, Lien-Fu
Li, Yun-Ju
author_facet Huang, Liang-Tsung
Wu, Chao-Chin
Lai, Lien-Fu
Li, Yun-Ju
author_sort Huang, Liang-Tsung
collection PubMed
description Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs). In this paper, we focused on how to improve the mapping, especially for short query sequences, by better usage of shared memory. We performed and evaluated the proposed method on two different platforms (Tesla C1060 and Tesla K20) and compared it with two classic methods in CUDASW++. Further, the performance on different numbers of threads and blocks has been analyzed. The results showed that the proposed method significantly improves Smith-Waterman algorithm on CUDA-enabled GPUs in proper allocation of block and thread numbers.
format Online
Article
Text
id pubmed-4538332
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher Hindawi Publishing Corporation
record_format MEDLINE/PubMed
spelling pubmed-45383322015-09-03 Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs Huang, Liang-Tsung Wu, Chao-Chin Lai, Lien-Fu Li, Yun-Ju Biomed Res Int Research Article Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs). In this paper, we focused on how to improve the mapping, especially for short query sequences, by better usage of shared memory. We performed and evaluated the proposed method on two different platforms (Tesla C1060 and Tesla K20) and compared it with two classic methods in CUDASW++. Further, the performance on different numbers of threads and blocks has been analyzed. The results showed that the proposed method significantly improves Smith-Waterman algorithm on CUDA-enabled GPUs in proper allocation of block and thread numbers. Hindawi Publishing Corporation 2015 2015-08-03 /pmc/articles/PMC4538332/ /pubmed/26339591 http://dx.doi.org/10.1155/2015/185179 Text en Copyright © 2015 Liang-Tsung Huang et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Huang, Liang-Tsung
Wu, Chao-Chin
Lai, Lien-Fu
Li, Yun-Ju
Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
title Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
title_full Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
title_fullStr Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
title_full_unstemmed Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
title_short Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
title_sort improving the mapping of smith-waterman sequence database searches onto cuda-enabled gpus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538332/
https://www.ncbi.nlm.nih.gov/pubmed/26339591
http://dx.doi.org/10.1155/2015/185179
work_keys_str_mv AT huangliangtsung improvingthemappingofsmithwatermansequencedatabasesearchesontocudaenabledgpus
AT wuchaochin improvingthemappingofsmithwatermansequencedatabasesearchesontocudaenabledgpus
AT lailienfu improvingthemappingofsmithwatermansequencedatabasesearchesontocudaenabledgpus
AT liyunju improvingthemappingofsmithwatermansequencedatabasesearchesontocudaenabledgpus