Speeding up index construction with GPU for DNA data sequences

• 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

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.