A review: FPGA based word matching stage of BLASTN

Author

Bhalekar, Sneha R. ; Chilveri, P.G.

Author_Institution

Dept. of E&TC, Smt. Kashibai Navale Coll. of Eng., Pune, India

fYear

2015

fDate

8-10 Jan. 2015

Firstpage

1

Lastpage

4

Abstract

Molecular Biologists use Basic Local Alignment Search Tool (BLAST) as one of the most popular sequences analysis tool. BLAST is a design used to efficiently find similar regions between the two sequences that have biological significance. As the size of genome sequences is increasing rapidly, the computation time of BLAST is continuously increasing to perform a complete genomic database search. Hence there is a need to accelerate this search process. In this paper, a new approach is proposed to scan the genomic sequence databases of Deoxyribonucleic Acid (DNA) using field programmable gate array (FPGA) based hardware. To accelerate the word matching stage of BLASTN, specifically designed for DNA sequences, and to derive its efficient architecture, a reconfigurable architecture is proposed.

Keywords

bioinformatics; database management systems; field programmable gate arrays; genomics; information retrieval; reconfigurable architectures; BLASTN; DNA sequences; FPGA based word matching stage; basic local alignment search tool; computation time; deoxyribonucleic acid; field programmable gate array; genome sequences; genomic database search; genomic sequence database scanning; reconfigurable architecture; sequences analysis tool; similar region finding; Acceleration; Bioinformatics; DNA; Databases; Field programmable gate arrays; Genomics; Matched filters; BLASTN; Bloom Filter; DNA sequences; Genomic Sequence analysis; reconfigurable computing;

fLanguage

English

Publisher

ieee

Conference_Titel

Pervasive Computing (ICPC), 2015 International Conference on

Conference_Location

Pune

Type

conf

DOI

10.1109/PERVASIVE.2015.7087107

Filename

7087107