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Fast Construction of Suffix Arrays for DNA Strings  

Jo, Jun-Ha ((주)소암시스템 연구소)
Kim, Nam-Hee (한양대학교 전자통신컴퓨터공학부)
Kwon, Ki-Ryong (부경대학교 컴퓨터공학과)
Kim, Dong-Kyue (한양대학교 전자통신컴퓨터공학부)
Publication Information
Journal of KIISE:Computer Systems and Theory / v.34, no.8, 2007 , pp. 319-326 More about this Journal
Abstract
To perform fast searching in massive data such as DNA strings, the most efficient method is to construct full-text index data structures of given strings. The widely used full-text index structures are suffix trees and suffix arrays. Since the suffix may uses less space than the suffix tree, the suffix array is proper for DNA strings. Previously developed construction algorithms of suffix arrays are not suitable for DNA strings since those are designed for integer alphabets. We propose a fast algorithm to construct suffix arrays on DNA strings whose alphabet sizes are fixed by 4. We reduce the construction time by improving encoding and merging steps on Kim et al.[1]'s algorithm. Experimental results show that our algorithm constructs suffix arrays on DNA strings 1.3-1.6 times faster than Kim et al.'s algorithm, and also for other algorithms in most cases.
Keywords
full-text index data structures; suffix arrays; DNA strings;
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