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Author Sandes, Edans Flavius De Oliveira ♦ Boukerche, Azzedine ♦ Melo, Alba Cristina Magalhaes Alves De
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2016
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword CellBE ♦ FPGA ♦ GPU ♦ Intel Phi ♦ Parallel algorithms ♦ Biological sequence comparison ♦ Multicores
Abstract Many bioinformatics applications, such as the optimal pairwise biological sequence comparison, demand a great quantity of computing resource, thus are excellent candidates to run in high-performance computing (HPC) platforms. In the last two decades, a large number of HPC-based solutions were proposed for this problem that run in different platforms, targeting different types of comparisons with slightly different algorithms and making the comparative analysis of these approaches very difficult. This article proposes a classification of parallel optimal pairwise sequence comparison solutions, in order to highlight their main characteristics in a unified way. We then discuss several HPC-based solutions, including clusters of multicores and accelerators such as Cell Broadband Engines (CellBEs), Field-Programmable Gate Arrays (FPGAs), Graphics Processing Units (GPUs) and Intel Xeon Phi, as well as hybrid solutions, which combine two or more platforms, providing the actual landscape of the main proposals in this area. Finally, we present open questions and perspectives in this research field.
ISSN 03600300
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2016-03-01
Publisher Place New York
e-ISSN 15577341
Journal ACM Computing Surveys (CSUR)
Volume Number 48
Issue Number 4
Page Count 36
Starting Page 1
Ending Page 36

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Source: ACM Digital Library