Systolic processing element based on the Viterbi algorithm for DNA sequence alignment

Author

Saliman, Nur Farah Ain ; Sabri, Nur Dalilah Ahmad ; Al Junid, Syed Abdul Mutalib ; Md Tahir, Nooritawati ; Majid, Zulkifli Abd

Author_Institution

Fac. of Electr. Eng., Univ. Teknol. MARA, Shah Alam, Malaysia

fYear

2013

fDate

13-15 Dec. 2013

Firstpage

268

Lastpage

274

Abstract

This paper presents the potential of the one-dimensional systolic processing element of the Viterbi algorithm in optimizing the DNA sequence alignment system processing engine. The objective of this paper was to optimize the sensitive DNA sequence alignment algorithm toward improving the performance and design complexity. In addition, theoretical study, design, and simulation were conducted using the Altera Quartus II version 9.1 software. The proposed architecture has been tested and is capable of accelerating more than 32 bits of input. As a conclusion, the proposed systolic design has been proven and is able to optimize the performance and design complexity of the most sensitive DNA sequence alignment algorithm on hardware-based accelerator platform.

Keywords

DNA; bioinformatics; parallel algorithms; systolic arrays; Altera Quartus II version 9.1 software; DNA sequence alignment system processing engine; Viterbi algorithm; design complexity; hardware-based accelerator platform; one-dimensional systolic processing element; sensitive DNA sequence alignment algorithm; systolic design; DNA; Silicon; DNA; Viterbi algorithm; sequence alignment;

fLanguage

English

Publisher

ieee

Conference_Titel

Systems, Process & Control (ICSPC), 2013 IEEE Conference on

Conference_Location

Kuala Lumpur

Print_ISBN

978-1-4799-2208-6

Type

conf

DOI

10.1109/SPC.2013.6735145

Filename

6735145