SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences.

ABSTRACT:

Background

The Smith-Waterman (SW) algorithm is the best choice for searching similar regions between two DNA or protein sequences. However, it may become impracticable in some contexts due to its high computational demands. Consequently, the computer science community has focused on the use of modern parallel architectures such as Graphics Processing Units (GPUs), Xeon Phi accelerators and Field Programmable Gate Arrays (FGPAs) to speed up large-scale workloads.

Results

This paper presents and evaluates SWIFOLD: a Smith-Waterman parallel Implementation on FPGA with OpenCL for Long DNA sequences. First, we evaluate its performance and resource usage for different kernel configurations. Next, we carry out a performance comparison between our tool and other state-of-the-art im

SUBMITTER: Rucci E 

PROVIDER: S-EPMC6245597 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature