Multi-pattern Matching with Bidirectional Indexes

Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko

doi:10.1007/978-3-642-32241-9_33

Cited by 6 publications

(7 citation statements)

References 18 publications

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“…Each implementation uses one specific type of data structure to represent FOS and BAS (but the same for both). We compared the following methodologies: AFA (which we implemented following Strothmann's description [24], since we did not find an available implementation); BIDWT (a wrap implementation using the sdsl library [11], which includes the bidirectional backward and forward search presented in [22]); ACAT; ACATS (using as sample parameter z = 1); ACATN (based on the work of Gog et al [10]); RACATN (our reduced version of ACATN); and SCAT.…”

Section: Resultsmentioning

confidence: 99%

“…Albrecht and Heun [3] studied how to optimally obtain the ALink in this case using binary search. A faster approach was presented by Gog et al [10]. As the procedure is symmetrical for a node BAS or of FOS, we explain it for the latter.…”

Section: A Classification Of Bi-directional Indexesmentioning

confidence: 99%

“…We refer to this approach as ACATN. For more details of how the array A is stored and queried, we refer the reader to [10].…”

Section: A Classification Of Bi-directional Indexesmentioning

confidence: 99%

“…We propose new Compressed Affix Tree indexes in both categories: the Asynchronous Compressed Affix Tree (ACAT) and the Synchronous Compressed Affix Tree (SCAT), and explain their practical implementations. Moreover, we exhibit both a reduced version of the index of [10], and a sampled version of ACAT. To evaluate the potential of these approaches and to compare them with different indexes for bidirectional search, we have implemented the Affix Array [24] (given that the original was not found), and compared seven indexing structures in practice.…”

Section: Introductionmentioning

confidence: 99%

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Full Compressed Affix Tree Representations

Cánovas

Rivals

2017

2017 Data Compression Conference (DCC)

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The Suffix Tree, a crucial and versatile data structure for string analysis of large texts, is often used in pattern matching and in bioinformatics applications. The Affix Tree generalizes the Suffix Tree in that it supports full tree functionalities in both search directions. The bottleneck of Affix Trees is their space requirement for storing the data structure. Here, we discuss existing representations and classify them into two categories: Synchronous and Asynchronous. We design Compressed Affix Tree indexes in both categories and explored how to support all tree operations bidirectionally. This work compares alternative approaches for compress the Affix Tree, measuring their space and time trade-offs for different operations. Moreover, to our knowledge, this is the first work that compares all Compressed Affix Tree implementations, i.e., four different approaches: the Affix Array, the Bidirectional Wavelet Index, and our two new structures, measures their space and time trade-offs, offering a practical benchmark for this structure.

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Section: Resultsmentioning

confidence: 99%

Section: A Classification Of Bi-directional Indexesmentioning

confidence: 99%

“…We refer to this approach as ACATN. For more details of how the array A is stored and queried, we refer the reader to [10].…”

Section: A Classification Of Bi-directional Indexesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Full Compressed Affix Tree Representations

Cánovas

Rivals

2017

2017 Data Compression Conference (DCC)

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“…For example, network intrusion detection systems monitor packets flowing on the network to protect computer systems from malicious access [3,4]. String search is also useful for locating specific amino acid sequences in biological databases [5,6,7].…”

Section: Introductionmentioning

confidence: 99%

A bit-parallel algorithm for searching multiple patterns with various lengths

Kusudo

Ino

Hagihara

2015

Journal of Parallel and Distributed Computing

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Smaller Fully-Functional Bidirectional BWT Indexes

Belazzougui

Cunial

2020

String Processing and Information Retrieval

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Given a string T on an alphabet of size σ, we describe a bidirectional Burrows-Wheeler index that takes O(|T | log σ) bits of space, and that supports the addition and removal of one character, on the left or right side of any substring of T , in constant time. Previously known data structures that used the same space allowed constant-time addition to any substring of T , but they could support removal only from specific substrings of T . We also describe an index that supports bidirectional addition and removal in O(log log |T |) time, and that takes a number of words proportional to the number of left and right extensions of the maximal repeats of T . We use such fully-functional indexes to implement bidirectional, frequency-aware, variable-order de Bruijn graphs with no upper bound on their order, and supporting natural criteria for increasing and decreasing the order during traversal.

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Multi-pattern Matching with Bidirectional Indexes

Cited by 6 publications

References 18 publications

Full Compressed Affix Tree Representations

Full Compressed Affix Tree Representations

A bit-parallel algorithm for searching multiple patterns with various lengths

Smaller Fully-Functional Bidirectional BWT Indexes

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