Paper Info
Title
Parallel Megabase DNA Sequence Comparison with OpenCL.
Abstract
Biological sequence comparison is a very common task in Bioinformatics applications. Many parallel solutions have been proposed for this problem, using different HPC platforms, programmed usually with platform-specific languages and frameworks. With this approach, it is difficult to port solutions among different platforms such as CPUs and GPUs, for instance. To tackle this problem, this paper proposes and evaluates an OpenCL parallel solution for Biological Sequence Comparison, which was integrated to the CUDAlign Megabase Sequence Comparison tool. The evaluation of our solution shows we were able to obtain a program for CPUs and GPUs (NVidia and AMD) with basically the same OpenCL code. In addition, in the comparison with SW# and CUDAlign optimized CUDA codes, we show that the performance of our OpenCL version has comparable and, many times, superior performance.
Year
DOI
Venue
2015
10.1109/HiPC.2015.13
HiPC
Keywords
Field
DocType
Parallel Programming,Biological Sequence Comparison,Graphical Processor Units (GPUs),OpenCL
Kernel (linear algebra),Computer science,CUDA,Parallel computing,General-purpose computing on graphics processing units,DNA sequencing
Conference
Citations 
PageRank 
References 
0
0.34
12
Authors
3
Name
Order
Citations
PageRank
Marco Antonio C. de Figueiredo110.70
Edans Sandes21298.94
Alba Cristina Magalhaes Alves De Melo325333.90