r-indexing the eBWT

IF 0.8 4区计算机科学 Q3 COMPUTER SCIENCE, THEORY & METHODS

Information and Computation Pub Date : 2024-03-05 DOI:10.1016/j.ic.2024.105155

Christina Boucher , Davide Cenzato , Zsuzsanna Lipták , Massimiliano Rossi , Marinella Sciortino

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引用次数: 0

Abstract

The extended Burrows-Wheeler Transform (eBWT) [Mantaci et al. TCS 2007] is a variant of the BWT, introduced for collections of strings. In this paper, we present the extended r-index, an analogous data structure to the r-index [Gagie et al. JACM 2020]. It occupies $O (r)$ words, with r the number of runs of the eBWT, and offers the same functionalities as the r-index. We also show how to efficiently support finding maximal exact matches (MEMs). We implemented the extended r-index and tested it on circular bacterial genomes and plasmids, comparing it to five state-of-the-art compressed text indexes. While our data structure maintains similar time and memory requirements for answering pattern matching queries as the original r-index, it is the only index in the literature that can naturally be used for both circular and linear input collections. This is an extended version of [Boucher et al., r-indexing the eBWT, SPIRE 2021].

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eBWT 的 r 索引

扩展 Burrows-Wheeler 变换（eBWT）是由 Mantaci 等人[TCS 2007]提出的，目的是将 BWT 的定义扩展到字符串集合。与其他常用的字符串集合 BWT 变体不同，eBWT 与字符串集合中字符串的输入顺序无关，同时保留了经典 BWT 的全部功能和可压缩性。在我们之前的工作[Boucher et al. eBWT , SPIRE 2021]中，我们提出了一种构建 eBWT 的线性时间算法。该算法结合了对后缀阵列诱导排序（SAIS）算法 [Nong 等人，IEEE Trans Comput 2011] 的修改和无前缀解析 [Boucher 等人，Alg Mol Biol 2019；Kuhnle 等人，JCB 2020]。

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来源期刊

Information and Computation 工程技术-计算机：理论方法

CiteScore

2.30

自引率

0.00%

发文量

119

审稿时长

140 days

期刊介绍： Information and Computation welcomes original papers in all areas of theoretical computer science and computational applications of information theory. Survey articles of exceptional quality will also be considered. Particularly welcome are papers contributing new results in active theoretical areas such as -Biological computation and computational biology- Computational complexity- Computer theorem-proving- Concurrency and distributed process theory- Cryptographic theory- Data base theory- Decision problems in logic- Design and analysis of algorithms- Discrete optimization and mathematical programming- Inductive inference and learning theory- Logic & constraint programming- Program verification & model checking- Probabilistic & Quantum computation- Semantics of programming languages- Symbolic computation, lambda calculus, and rewriting systems- Types and typechecking