NDLI: GPU technology as a platform for accelerating local complexity analysis of protein sequences

Content Provider	IEEE Xplore Digital Library
Author	Papadopoulos, A. Kirmitzoglou, I. Promponas, V.J. Theocharides, T.
Copyright Year	2013
Description	Author affiliation: Dept. of Electr. & Comput. Eng., Univ. of Cyprus, Nicosia, Cyprus (Papadopoulos, A.; Theocharides, T.) \|\| Dept. of Biol. Sci., Univ. of Cyprus, Nicosia, Cyprus (Kirmitzoglou, I.; Promponas, V.J.)
Abstract	The use of GPGPU programming paradigm (running CUDA-enabled algorithms on GPU cards) in Bioinformatics showed promising results [1]. As such a similar approach can be used to speedup other algorithms such as CAST, a popular tool used for masking low-complexity regions (LCRs) in protein sequences [2] with increased sensitivity. We developed and implemented a CUDA-enabled version (GPU_CAST) of the multi-threaded version of CAST software first presented in [3] and optimized in [4]. The proposed software implementation uses the nVIDIA CUDA libraries and the GPGPU programming paradigm to take advantage of the inherent parallel characteristics of the CAST algorithm to execute the calculations on the GPU card of the host computer system. The GPU-based implementation presented in this work, is compared against the multi-threaded, multi-core optimized version of CAST [4] and yielded speedups of 5x-10x for large protein sequence datasets.
Starting Page	2684
Ending Page	2687
File Size	243683
Page Count	4
File Format	PDF
ISBN	9781457702167
ISSN	1557170X
DOI	10.1109/EMBC.2013.6610093
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-07-03
Publisher Place	Japan
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Graphics processing units Bioinformatics Kernel Programming Proteins Algorithm design and analysis Databases
Content Type	Text
Resource Type	Article
Subject	Signal Processing Biomedical Engineering Health Informatics Computer Vision and Pattern Recognition

Sl.	Authority	Responsibilities	Communication Details
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
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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