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A Storage-Efficient Suffix Tree Construction Algorithm for Human Genome Sequences
Woong-Kee LOH Heejune AHN
IEICE TRANSACTIONS on Information and Systems
Publication Date: 2011/12/01
Online ISSN: 1745-1361
Print ISSN: 0916-8532
Type of Manuscript: LETTER
Category: Biological Engineering
storage-efficient suffix tree, human genome sequences, divide-and-conquer,
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The suffix tree is one of most widely adopted indexes in the application of genome sequence alignment. Although it supports very fast alignment, it has a couple of shortcomings, such as a very long construction time and a very large volume size. Loh et al.  proposed a suffix tree construction algorithm with dramatically improved performance; however, the size still remains as a challenging problem. We propose an algorithm by extending the one by Loh et al. to reduce the suffix tree size. As a result of our experiments, our algorithm constructed a suffix tree of approximately 60% of the size within almost the same time period.