NDLI: A scalable high-throughput pipeline architecture for DNA sequence alignment

Content Provider	IEEE Xplore Digital Library
Author	Ghosh, S. Mandal, S. Saha Ray, S.
Copyright Year	2015
Description	Author affiliation: Dept. of Inf. Technol., St. Thomas' Coll. of Eng. & Technol., Kolkata, India (Saha Ray, S.) \|\| Dept. of Comput. Sci. & Technol., Indian Inst. of Eng. Sci. & Technol., Shibpur, India (Ghosh, S.; Mandal, S.)
Abstract	A novel scalable architecture for DNA sequence alignment has been presented in this paper. A pipelined architecture with a dedicated backtrack processor have been designed for fast and sophisticated DNA sequence alignment. Additionally, instead of using CAM which consumes huge power, this architecture efficiently uses RAM to boost the speed of DNA sequence alignment in real time. This architecture incorporates a pipeline structure for matrix fill operation to achieve temporal parallelism in preparing substitution matrix for a number of sequences and a backtrack processor to obtain aligned sequences. Besides, this paper presents a comparative analysis on the processing time of this architecture using three numerous cases based on temporal and special parallelism, namely, dedicated, moderately-dedicated and shared logic components. The complete architecture has been simulated for 1000 database sequences considering both 16 and 32 nucleotides as DNA sequence size.
Starting Page	1
Ending Page	6
File Size	1061910
Page Count	6
File Format	PDF
ISBN	9781479986392
ISSN	21593450
e-ISBN	9781479986415
DOI	10.1109/TENCON.2015.7373055
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-11-01
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Biology Global Alignment DNA Sequence Alignment Pipeline DNA Sequence Alignment Pipeline Matrix Fill-up Backtrack Processor
Content Type	Text
Resource Type	Article
Subject	Electrical and Electronic Engineering Computer Science Applications

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