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Speeding up index construction with GPU for DNA data sequences

The advancement of technology in scientific community has produced terabytes of biological data.This datum includes DNA sequences.String matching algorithm which is traditionally used to match DNA sequences now takes much longer time to execute because of the large size of DNA data and also the smal...

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Main Authors: Rahmaddiansyah, ,, Abdul Rashid, Nur’aini
Format: Conference or Workshop Item
Language:English
Published: 2011
Subjects:
QA76 Computer software
Online Access:http://repo.uum.edu.my/13623/1/92.pdf
http://repo.uum.edu.my/13623/
http://www.icoci.cms.net.my
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id my.uum.repo.13623
record_format eprints
spelling my.uum.repo.136232015-04-07T06:52:21Z http://repo.uum.edu.my/13623/ Speeding up index construction with GPU for DNA data sequences Rahmaddiansyah, , Abdul Rashid, Nur’aini QA76 Computer software The advancement of technology in scientific community has produced terabytes of biological data.This datum includes DNA sequences.String matching algorithm which is traditionally used to match DNA sequences now takes much longer time to execute because of the large size of DNA data and also the small number of alphabets.To overcome this problem, the indexing methods such as suffix arrays or suffix trees have been introduced.In this study we used suffix arrays as indexing algorithm because it is more applicable, not complex and used less space compared to suffix trees.The parallel method is then introduced to speed up the index construction process. Graphic processor unit (GPU) is used to parallelize a segment of an indexing algorithm. In this research, we used a GPU to parallelize the sorting part of suffix array construction algorithm.Our results show that the GPU is able to accelerate the process of building the index of the suffix array by 1.68 times faster than without GPU. 2011-06-24 Conference or Workshop Item PeerReviewed application/pdf en http://repo.uum.edu.my/13623/1/92.pdf Rahmaddiansyah, , and Abdul Rashid, Nur’aini (2011) Speeding up index construction with GPU for DNA data sequences. In: 3rd International Conference on Computing and Informatics (ICOCI 2011), 8-9 June 2011, Bandung, Indonesia. http://www.icoci.cms.net.my
institution Universiti Utara Malaysia
building UUM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Utara Malaysia
content_source UUM Institutionali Repository
url_provider http://repo.uum.edu.my/
language English
topic QA76 Computer software
spellingShingle QA76 Computer software
Rahmaddiansyah, ,
Abdul Rashid, Nur’aini
Speeding up index construction with GPU for DNA data sequences
description The advancement of technology in scientific community has produced terabytes of biological data.This datum includes DNA sequences.String matching algorithm which is traditionally used to match DNA sequences now takes much longer time to execute because of the large size of DNA data and also the small number of alphabets.To overcome this problem, the indexing methods such as suffix arrays or suffix trees have been introduced.In this study we used suffix arrays as indexing algorithm because it is more applicable, not complex and used less space compared to suffix trees.The parallel method is then introduced to speed up the index construction process. Graphic processor unit (GPU) is used to parallelize a segment of an indexing algorithm. In this research, we used a GPU to parallelize the sorting part of suffix array construction algorithm.Our results show that the GPU is able to accelerate the process of building the index of the suffix array by 1.68 times faster than without GPU.
format Conference or Workshop Item
author Rahmaddiansyah, ,
Abdul Rashid, Nur’aini
author_facet Rahmaddiansyah, ,
Abdul Rashid, Nur’aini
author_sort Rahmaddiansyah, ,
title Speeding up index construction with GPU for DNA data sequences
title_short Speeding up index construction with GPU for DNA data sequences
title_full Speeding up index construction with GPU for DNA data sequences
title_fullStr Speeding up index construction with GPU for DNA data sequences
title_full_unstemmed Speeding up index construction with GPU for DNA data sequences
title_sort speeding up index construction with gpu for dna data sequences
publishDate 2011
url http://repo.uum.edu.my/13623/1/92.pdf
http://repo.uum.edu.my/13623/
http://www.icoci.cms.net.my
_version_ 1644281236215037952
score 13.211869

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