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Suffix Array of Alignment: A Practical Index for Similar Data.

Title
Suffix Array of Alignment: A Practical Index for Similar Data.
Author
박희진
Keywords
Indexes for similar data; suffix arrays; alignments
Issue Date
2013-10
Publisher
Springer-Verlag Berlin Heidelberg 2013
Citation
String Processing & Information Retrieval, 2013, 8214, P.243-254
Abstract
The suffix tree of alignment is an index data structure for similar strings. Given an alignment of similar strings, it stores all suffixes of the alignment, called alignment-suffixes. An alignment-suffix represents one suffix of a string or suffixes of multiple strings starting at the same position in the alignment. The suffix tree of alignment makes good use of similarity in strings theoretically. However, suffix trees are not widely used in biological applications because of their huge space requirements, and instead suffix arrays are used in practice. In this paper we propose a space-economical version of the suffix tree of alignment, named the suffix array of alignment (SAA). Given an alignment ρ of similar strings, the SAA for ρ is a lexicographically sorted list of all the alignment-suffixes of ρ. The SAA supports pattern search as efficiently as the generalized suffix array. Our experiments show that our index uses only 14% of the space used by the generalized suffix array to index 11 human genome sequences. The space efficiency of our index increases as the number of the genome sequences increases. We also present an efficient algorithm for constructing the SAA. ⓒ Springer International Publishing 2013.
URI
https://link.springer.com/chapter/10.1007/978-3-319-02432-5_27http://hdl.handle.net/20.500.11754/51709
ISBN
978-3-319-02431-8; 978-3-319-02432-5
ISSN
1611-3349; 0302-9743
DOI
10.1007/978-3-319-02432-5_33
Appears in Collections:
COLLEGE OF ENGINEERING[S](공과대학) > COMPUTER SCIENCE(컴퓨터소프트웨어학부) > Articles
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