A parallel architecture for high speed BLAST using FPGA

Author

Mahmoodi, Mohammad Reza ; Nikaein, Hossein ; Fahimi, Zahra

Author_Institution

Dept. of Electr. & Comput. Eng., Isfahan Univ. of Technol., Isfahan, Iran

fYear

2014

fDate

20-22 May 2014

Firstpage

57

Lastpage

61

Abstract

Undoubtedly, Basic Local Alignment Search Tool is one of the most prevalent algorithms in sequence searching and bioinformatics. BLAST is an index-based approach in order to recognize an unknown string of DNA sequence and due to its high computational nature, different types of hardware configurations have been proposed. In this paper, the traditional algorithm is applied; however a new architecture is proposed to speed up the algorithm. The design consists of a workstation and a FPGA as an accelerator. The system is based on 41 parallel cores implemented on Xilinx XC4VFX100 FPGA device. The most appealing features of this design are its speed and long input streams. Queries and subjects up to thousands of characters are processed in this architecture and it is verified to be 75.1 faster than NCBI software run at 3GHz, Pentium4 system.

Keywords

bioinformatics; field programmable gate arrays; genetics; software architecture; BLAST; DNA sequence searching; Xilinx XC4VFX100 FPGA device; basic local alignment search tool; bioinformatics; parallel architecture; Algorithm design and analysis; Computer architecture; Field programmable gate arrays; Indexes; Random access memory; Software; BLAST Algorithm; FPGA; Hardware Implementation; Sequence Searching;

fLanguage

English

Publisher

ieee

Conference_Titel

Electrical Engineering (ICEE), 2014 22nd Iranian Conference on

Conference_Location

Tehran

Type

conf

DOI

10.1109/IranianCEE.2014.6999503

Filename

6999503