FM-index of alignment: A compressed index for similar strings
- Authors
- Na, Joong Chae; Kim, Hyunjoon; Park, Heejin; Lecroq, Thierry; Leonard, Martine; Mouchard, Laurent; Park, Kunsoo
- Issue Date
- Jul-2016
- Publisher
- ELSEVIER SCIENCE BV
- Keywords
- Indexes for similar strings; FM-indexes; Suffix arrays; Alignments; Backward search
- Citation
- THEORETICAL COMPUTER SCIENCE, v.638, pp.159 - 170
- Indexed
- SCIE
SCOPUS
- Journal Title
- THEORETICAL COMPUTER SCIENCE
- Volume
- 638
- Start Page
- 159
- End Page
- 170
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/154336
- DOI
- 10.1016/j.tcs.2015.08.008
- ISSN
- 0304-3975
- Abstract
- In this paper we propose the FM-index of alignment, a compressed index for similar strings with the functionalities of pattern search and random access. For this, we first design a new and improved version of the suffix array of alignment. The FM-index of alignment is an FM-index of this suffix array of alignment. The FM-index of alignment supports the LF-mapping and backward search, the key functionalities of the FM-index, but the LF-mapping and backward search of our index is significantly more involved than the original FM index. We implemented the FM-index of alignment and did experiments on 100 genome sequences from the 1000 Genomes Project. The index size of the FM-index of alignment is about a half of that of RLCSA due to Makinen et al.
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