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Bi-Directional r-Indexes

Authors Yuma Arakawa, Gonzalo Navarro, Kunihiko Sadakane

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Subject Classification

ACM Subject Classification
  • Theory of computation → Data compression
Keywords
  • Compressed text indexes
  • Burrows-Wheeler Transform
  • highly repetitive text collections

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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.

Cite As Get BibTex

Yuma Arakawa, Gonzalo Navarro, and Kunihiko Sadakane. Bi-Directional r-Indexes. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 11:1-11:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022) https://doi.org/10.4230/LIPIcs.CPM.2022.11

Author Details

Yuma Arakawa
  • Department of Mathematical Informatics, The University of Tokyo, Japan
Gonzalo Navarro
  • CeBiB and Department of Computer Science, University of Chile, Santiago, Chile
Kunihiko Sadakane
  • Department of Mathematical Informatics, The University of Tokyo, Japan

Funding

  • Navarro, Gonzalo: Funded in part by Basal Funds FB0001 and Fondecyt Grant 1-200038, ANID, Chile.

Supplementary Materials

References

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