Design and Implementation of high-performance sequence analysis environment using GPGPU

基于GPGPU的高性能序列分析环境的设计与实现

• 批准号: 21510217
• 负责人: SUETSUGU Yoshitaka
• 金额: $ 2.25万
• 依托单位: National Institute of Agrobiological Sciences
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2009
• 资助国家: 日本
• 起止时间: 2009 至 2011
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21510217/
• 关键词: 情報工学; 配列解析; 並列処理; ゲノム; GPGPU; バイオインフォマティクス

Since the emergence of high-throughput sequencing platform, the cost for both experimental and time were much reduced for DNA sequencing. This makes easy to produce enormous amount of DNA data. As the result, analyzing huge sequence database has become a next target to find an e & cient solution. To overcome this problem, we applied General Purpose computation on Graphic Processing Unit(GPGPU) for sequence analysis. We implemented several algorithms including Smith-Waterman algorithm based on GPGPU. The GPU-based programs showed higher performance compared to CPU-based ones.

自从高通量测序平台的出现，DNA测序的实验成本和时间成本都大大降低。这使得生成大量 DNA 数据变得容易。因此，分析庞大的序列数据库已成为寻找高效解决方案的下一个目标。为了克服这个问题，我们在图形处理单元（GPGPU）上应用通用计算来进行序列分析。我们实现了多种算法，包括基于GPGPU的Smith-Waterman算法。与基于 CPU 的程序相比，基于 GPU 的程序表现出更高的性能。

项目成果

MULTI-GPUsによる高速配列解析環境の構築

使用 MULTI-GPU 构建高速序列分析环境

• 发表时间: 2010
• 作者: T. Maeshiro;S. Nakayama;Yasuhide Okuyama;真栄城哲也;Yasuhide Okuyama;Yasuhide Okuyama;Yasuhide Okuyama;Yasuhide Okuyama;Yasuhide Okuyama and Stephanie E. Chang.;平田一樹,太田信行,上樂明也,広井賀子,舟橋啓,末次克行
• 通讯作者: 平田一樹,太田信行,上樂明也,広井賀子,舟橋啓,末次克行

Design and Implementation of high-performance sequence analysis environment using GPGPU

基于GPGPU的高性能序列分析环境的设计与实现

• 发表时间: 2009
• 作者: Kazuki Hirata;Nobuyuki Ohta;Noriko Hiroi;Akira Funahashi;Yoshitaka Suetsugu
• 通讯作者: Yoshitaka Suetsugu