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Comparison Architecture for Large Number of Genomic Sequences  

Choi, Hae-won (Department of Computer Engineering, Kyungwoon University)
Ryoo, Myung-Chun (Department of Computer Engineering, Kyungwoon University)
Park, Joon-Ho (Department of Computer Engineering, Kyungwoon University)
Publication Information
Journal of Information Technology and Architecture / v.9, no.1, 2012 , pp. 11-19 More about this Journal
Abstract
Generally, a suffix tree is an efficient data structure since it reveals the detailed internal structures of given sequences within linear time. However, it is difficult to implement a suffix tree for a large number of sequences because of memory size constraints. Therefore, in order to compare multi-mega base genomic sequence sets using suffix trees, there is a need to re-construct the suffix tree algorithms. We introduce a new method for constructing a suffix tree on secondary storage of a large number of sequences. Our algorithm divides three files, in a designated sequence, into parts, storing references to the locations of edges in hash tables. To execute experiments, we used 1,300,000 sequences around 300Mbyte in EST to generate a suffix tree on disk.
Keywords
suffix tree; large data sets; sequence analysis; genomic sequences;
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