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A Fast Parallel Algorithm for Indexing Human Genome Sequences
- Authors
- Loh, Woong-Kee; Han, Kyoung-Soo
- Issue Date
- May-2014
- Publisher
- IEICE-INST ELECTRONICS INFORMATION COMMUNICATIONS ENG
- Keywords
- human genome sequences; suffix tree; parallel algorithm; suffix array; disk-based index
- Citation
- IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, v.E97D, no.5, pp.1345 - 1348
- Journal Title
- IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS
- Volume
- E97D
- Number
- 5
- Start Page
- 1345
- End Page
- 1348
- ISSN
- 1745-1361
- Abstract
- A suffix tree is widely adopted for indexing genome sequences. While supporting highly efficient search, the suffix tree has a few shortcomings such as very large size and very long construction time. In this paper, we propose a very fast parallel algorithm to construct a disk-based suffix tree for human genome sequences. Our algorithm constructs a suffix array for part of the suffixes in the human genome sequence and then converts it into a suffix tree very quickly. It outperformed the previous algorithms by Loh et al. and Barsky et al. by up to 2.09 and 3.04 times, respectively.
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Related Researcher
- Loh, Woong Kee
- College of IT Convergence (Department of Software)