NDLI: Parallelization of RNA secondary structure prediction algorithm on multicore

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Parallelization of RNA secondary structure prediction algorithm on multicore

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Parallelization of RNA secondary structure prediction algorithm on multicore

Content Provider	ACM Digital Library
Author	Mahajan, Anjali Chaudhari, Narendra
Abstract	RNA secondary structure prediction is invaluable in creating new drugs and understanding genetic diseases, in gene expression and regulation. RNA molecules have proven their clinically consequential deep inroads into the biological functions. Needless to mention about the role of even small RNA's with numerous nucleotides which does the function of gene splicing, editing, and regulation. There is accelerating increase of data set sizes originating from powerful high-throughput measuring devices in Bioinformatics, A major limiting factor in achieving good performance on modern architectures is memory latency and bandwidth. The cost of computation is very less than the cost of moving data from main memory. This disparity between communication and computation costs has compelled the programmers to make changes in the ways algorithms are designed. A promising solution to speed up sequential programs, which are difficult to parallelise otherwise is through Speculative parallelisation. This paper proposes a new software-only speculative parallelization scheme for implementing RNA Secondary Structure Prediction algorithm in parallel. The scheme is developed after a systematic evaluation of the design options available. It is also shown to be efficient, robust and to outperform previously proposed schemes used for parallel implementation of RNA Secondary Structure Prediction.
Starting Page	1
Ending Page	6
Page Count	6
File Format	PDF
ISBN	9781605588148
DOI	10.1145/2675744.2675765
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-10-09
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Rna secondary structure prediction Speculative parallelization
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
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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