NDLI: GPU accelerated inexact matching for multiple patterns in DNA sequences

Content Provider	IEEE Xplore Digital Library
Author	Rastogi, P. Guddeti, R.
Copyright Year	2014
Description	Author affiliation: Dept. of Inf. Technol., Nat. Inst. of Technol., Mangalore, India (Rastogi, P.; Guddeti, R.)
Abstract	DNA sequencing technology generates millions of patterns on Every run of the machine and it poses a challenge for matching these patterns to the reference genome effectively with high execution speed. The main idea here is inexact matching of patterns with mismatches and gaps (insertions and deletions). In Inexact match up pattern DNA sequence is to be matched with some allowed number of errors. Here we have considered 2 errors. Errors can be mismatches or gaps. Existing algorithm as SOAP3 performs inexact matching on GPU with mismatches only. SOAP3 doesn't consider gaps (insertion and deletion). General Purpose Graphical Processing Unit (GPGPU) is an effective solution in terms of the cost and speed and there by providing a high degree of parallelism. This paper presents a parallel implementation of multiple pattern inexact matching in genome reference using CUDA based on BWT. The algorithm incorporates DFS (Depth First Search) Strategy for For matching multiple patterns, each thread of GPGPU is provided with a different pattern and hence millions of patterns can be matched using only one CUDA kernel. Since the memory of the GPU is limited then memory management should handled carefully. Synchronization of multiple threads is provided in order to prevent illegal access to the shared memory. GPU results are compared with that of CPU execution Experimental results of the proposed methodology achieved an average speedup factor of seven as compared to that of CPU execution.
Starting Page	163
Ending Page	167
File Size	185862
Page Count	5
File Format	PDF
ISBN	9781479930784
e-ISBN	9781479930807
DOI	10.1109/ICACCI.2014.6968404
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2014-09-24
Publisher Place	India
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Pattern Matching Instruction sets Memory management Graphics processing units Genomics DNA Parallel Computing Bioinformatics Pattern matching GPGPU
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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