NDLI: A reconfigurable embedded system for sequence alignment problem

Content Provider	IEEE Xplore Digital Library
Author	Hsing-Lung Chen Fu-Hui Cheng Shu-Hua Hu
Copyright Year	2011
Description	Author affiliation: Department of Computer Science and Information Engineering, Jiwen University of Science and Tech., Taipei, Taiwan (Shu-Hua Hu) \|\| Department of Electronic Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan (Hsing-Lung Chen; Fu-Hui Cheng)
Abstract	Sequence alignment is a basic and important tool for the research of biological information. It can compare and analyze the degree of similarity between two or more sequences to speculate whether they are derived from the common ancestor or not. Usually, lengths of both input sequences are fairly long, resulting in long processing time. Many previous algorithms have been proposed to reduce the processing time. Previous systolic algorithms can achieve linear time complexity with linear number of processing elements. However, each processing element needs linear memory-space to store intermediate results and then the system needs too large memory-space in total, resulting in being not suitable for being implemented on VLSI. Hence, to design an efficient and hardware-implementable algorithm is an important issue. This paper proposes a reconfigurable systolic architecture for the sequence alignment problem. At first, we use Needleman-Wunsch recursive function to derive the rules of forward and backward processes. By employing “divide and conquer” technique, we can find a sequence alignment with the best score. It needs a little more time complexity with only linear memory-space in total. Furthermore, the number of physical processing elements can be fixed by employing the concept of virtual processing elements. Therefore, our proposed reconfigurable systolic architecture is not only hardware-implementable on VLSI but also efficient.
Starting Page	1345
Ending Page	1351
File Size	283030
Page Count	7
File Format	PDF
ISBN	9781457703058
ISSN	21601348
e-ISBN	9781457703089
DOI	10.1109/ICMLC.2011.6016879
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-07-10
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Complexity theory Program processors Arrays Process control Machine learning Cybernetics DNA Reconfigurable Sequence alignment Systolic algorithm Divide and conquer Virtual processing elements
Content Type	Text
Resource Type	Article

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