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DOI: 10.4230/LIPIcs.CPM.2022.11
URN: urn:nbn:de:0030-drops-161386
URL: https://drops.dagstuhl.de/opus/volltexte/2022/16138/
Arakawa, Yuma ; Navarro, Gonzalo ; Sadakane, Kunihiko
Bi-Directional r-Indexes
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Abstract
Indexing highly repetitive texts is important in fields such as bioinformatics and versioned repositories. The run-length compression of the Burrows-Wheeler transform (BWT) provides a compressed representation particularly well-suited to text indexing. The r-index is one such index. It enables fast locating of occurrences of a pattern within O(r) words of space, where r is the number of equal-letter runs in the BWT. Its mechanism of locating is to maintain one suffix array sample along the backward-search of the pattern, and to compute all the pattern positions from that sample once the backward-search is complete. In this paper we develop this algorithm further, and propose a new bi-directional text index called the br-index, which supports extending the matched pattern both in forward and backward directions, and locating the occurrences of the pattern at any step of the search, within O(r+r_R) words of space, where r_R is the number of equal-letter runs in the BWT of the reversed text. Our experiments show that the br-index captures the long repetitions of the text, and outperforms the existing indexes in text searching allowing some mismatches except in an internal part.
BibTeX - Entry
@InProceedings{arakawa_et_al:LIPIcs.CPM.2022.11,
author = {Arakawa, Yuma and Navarro, Gonzalo and Sadakane, Kunihiko},
title = {{Bi-Directional r-Indexes}},
booktitle = {33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
pages = {11:1--11:14},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-234-1},
ISSN = {1868-8969},
year = {2022},
volume = {223},
editor = {Bannai, Hideo and Holub, Jan},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/opus/volltexte/2022/16138},
URN = {urn:nbn:de:0030-drops-161386},
doi = {10.4230/LIPIcs.CPM.2022.11},
annote = {Keywords: Compressed text indexes, Burrows-Wheeler Transform, highly repetitive text collections}
}
| Keywords: | Compressed text indexes, Burrows-Wheeler Transform, highly repetitive text collections | |
| Seminar: | 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022) | |
| Issue date: | 2022 | |
| Date of publication: | 22.06.2022 | |
| Supplementary Material: | Software (Source Code): https://github.com/U-Ar/br-index archived at: https://archive.softwareheritage.org/swh:1:dir:988f1c8381e90fa759b316908113e0c5cf92f228 |
