Fast Index Construction Of Biological Data Using Graphics Processing Unit (GPU)

dc.contributor.author	Rahmaddiansyah
dc.date.accessioned	2017-10-20T07:38:37Z
dc.date.available	2017-10-20T07:38:37Z
dc.date.issued	2014-07
dc.description.abstract	Technological advancement is producing terabytes of biological data in the scientific community. Such data include deoxyribonucleic acid and protein sequences. String matching algorithm was traditionally used to match DNA sequences but requires a long time to execute because of the large size DNA and protein sequences. Indexing methods, such as suffix arrays (SA) and suffix trees (ST), have been introduced to remedy the processing problem. In this study, SA are used as an indexing algorithm because such SA are more applicable than ST. SA are not complex and are space efficient. The parallel method is introduced to accelerate the index construction process. Graphics Processing Unit is a processor used to parallelize a part of an indexing algorithm. This work shows how the GPU is used to sort parts of the SA construction algorithm. Results show that the GPU can accelerate the construction of SA. The use of a GPU can process DNA data 2.01 times faster and protein data 1.63 times faster than the case without a GPU.	en_US
dc.identifier.uri	http://hdl.handle.net/123456789/5033
dc.language.iso	en	en_US
dc.publisher	Universiti Sains Malaysia	en_US
dc.subject	Indexing technique	en_US
dc.title	Fast Index Construction Of Biological Data Using Graphics Processing Unit (GPU)	en_US
dc.type	Thesis	en_US

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