G-PAS 2.0 – an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs

Bulletin of the Polish Academy of Sciences. Technical Sciences

W. FrohmbergInstitute of Computing Science, Pozna? University of Technology, 3 Piotrowo St., 60-965 Pozna?, PolandOther articles by this author:De Gruyter OnlineGoogle Scholar¹  P. WojciechowskiCorresponding authorInstitute of Computing Science, Pozna? University of Technology, 3 Piotrowo St., 60-965 Pozna?, PolandEmailOther articles by this author:De Gruyter OnlineGoogle Scholar¹  J.BlazewiczInstitute of Computing Science, Pozna? University of Technology, 3 Piotrowo St., 60-965 Pozna?, Poland / Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Z. Noskowski St., 61-704 Pozna?, PolandOther articles by this author:De Gruyter OnlineGoogle Scholar²  M. KierzynkaInstitute of Computing Science, Pozna? University of Technology, 3 Piotrowo St., 60-965 Pozna?, Poland / Pozna? Supercomputing and Networking Center, 12/14 Z. Noskowski St., 61-704 Pozna?, PolandOther articles by this author:De Gruyter OnlineGoogle Scholar³ 

[1] Institute of Computing Science, Pozna? University of Technology, 3 Piotrowo St., 60-965 Pozna?, Poland;Institute of Computing Science, Pozna? University of Technology, 3 Piotrowo St., 60-965 Pozna?, Poland / Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Z. Noskowski St., 61-704 Pozna?, Poland;Institute of Computing Science, Pozna? University of Technology, 3 Piotrowo St., 60-965 Pozna?, Poland / Pozna? Supercomputing and Networking Center, 12/14 Z. Noskowski St., 61-704 Pozna?, Poland

关键词: Keywords : pairwise alignment;    GPU computing;    alignment with backtracking procedure.;   

DOI  :  10.2478/v10175-012-0062-1

学科分类：工程和技术（综合）

来源: Polska Akademia Nauk * Centrum Upowszechniania Nauki / Polish Academy of Sciences, Center for the Advancement of Science

【 摘 要 】

Several highly efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units). G-PAS (GPU-based Pairwise Alignment Software) was one of them, however, with a couple of interesting features that made it unique. Nevertheless, in order to adapt it to a new computational architecture some changes had to be introduced. In this paper we present G-PAS 2.0 - a new version of the software for performing high-throughput alignment. Results show, that the new version is faster nearly by a fourth on the same hardware, reaching over 20 GCUPS (Giga Cell Updates Per Second).

【 授权许可】

Unknown