Performance Evaluation for Field Programmable Gate Array-based Bioinformatics Sequence Alignment

Abstract

Sequence alignment is a computationally expensive activity in bioinformatics that can benefit significantly from Field Programmable Gate Array-based high-performance computing systems. This paper evaluates the performance of such systems for bioinformatics sequence alignment applications considering various parameters like data bus width (W), the number of processing elements, and the maximum operating frequency.

Keywords:

• Bioinformatics
• Field programmable gate arrays
• High performance computing
• Performance evaluation
• Sequence alignment

Additional information

Notes on contributors

Laiq Hasan

Laiq Hasan received his Ph.D. degree in Computer Engineering from Delft University of Technology, Delft, The Netherlands, in 2011. He received his M.Sc. degree and B.Sc. degree (with Honors) in Electrical Engineering from the University of Engineering and Technology, Peshawar, Pakistan, in 2003 and 2000 consecutively. He worked as a Visiting Researcher in the Faculty of Electrical Engineering Mathematics and Computer Science at Delft University of Technology, Delft, The Netherlands. He is chairman in the Department of Computer Systems Engineering at the University of Engineering and Technology, Peshawar, Pakistan. His research interests include logic design, computer architecture, bioinformatics, performance analysis, and optimizations. Besides publishing a technical book and a book chapter, he has authored and co-authored many research papers in journals of international repute. He has also presented his research work in various international conferences. E-mail: [email protected]

Mottaqiallah Taouil

Mottaqiallah Taouil is a PhD student within the Computer Engineering Laboratory, Faculty of Electrical Engineering, Mathematics and Computer Science at the Delft University of Technology, Delft, The Netherlands. He received his M.Sc. degree in Computer Engineering from Delft University of Technology, Delft, The Netherlands, in 2009. His research interests include 3D architectures, bioinformatics, (3D) design for testability, (3D) yield analysis, and 3D memory test structures. E-mail: [email protected]

Haseeb Zafar

Haseeb Zafar received the Ph.D. degree in Wireless Mobile Ad-hoc Networks from the University of Strathclyde, Glasgow, UK in 2009, the M.S. degree in Telecommunications and Computers from the George Washington University, Washington DC, USA in 2003 and the B.Sc. degree (with Honors) in Electrical Engineering from the University of Engineering and Technology, Peshawar, Pakistan in 1996. He carried one year postdoctoral research in the Department of Electronic & Electrical Engineering at the University of Strathclyde, Glasgow, UK with Professor Ivan Andonovic. Currently, he is an Assistant Professor in the Department of Computer Systems Engineering at the University of Engineering and Technology, Peshawar, Pakistan. His research interests include data communications, computer networks, computational bioinformatics, wireless communications and mobile ad hoc, sensor and mesh networks. He has authored and co-authored many research papers in journals of international repute including the IET Communications and IETE Technical Review. He has presented his research work in various international conferences. E-mail: [email protected]