Year: 2009
Type: article
Abstract: Recently, rapid growth of the technology of the Graphics Processing Unit (GPU) has led to a surge of interest in using the GPU for general purpose applications. We can utilize the GPU in computation as a massive parallel coprocessor because the GPU consists of multiple cores. The GPU is also an affordable, user-programmable, and attractive commodity. In bioinformatics, finding the similarities in protein and DNA sequence databases has become a fundamental procedure. The Smith-Waterman algorithm based on dynamic programming is one of the methods used to search for all of the possible local alignments between two sequences, enabling us to find the optimal local alignments. However, dynamic programming requires a sequential calculation due to data dependency. Also required are a high number of computation steps proportional to the product of the lengths of the two sequences. the CPU and on the single GPU. Therefore, the multiple GPUs are shown to be extremely efficient as a high computing accelerator for a bioinformatics application.
Source: BMC Bioinformatics
Author: Sungbo Jung
Institution: University of Louisville
Language: English
Subfield: Hardware and Architecture
Field: Computer Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,990
OpenAlex ID: W2109268917