Efficient Variants of the Backward-Oracle-Matching Algorithm

Faro, Simone; Lecroq, Thierry; Ea, Litis

doi:10.1142/s0129054109006991

Cited by 37 publications

(35 citation statements)

References 16 publications

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“…The extended backward oracle matching algorithm [19] was also proposed to handle long patterns and small alphabets. But the memory utilization of these algorithms was huge.…”

Section: Literature Reviewmentioning

confidence: 99%

An Intuitive Wizard to Identify Pattern in Similarity Expressed Gene Set of Rice

Barrow¹,

Naryanan²

2018

IJIES

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While the genome sequences of different crops have been published and annotated, relatively little is known about the transcriptional networks that regulate gene expression. There are different ways of finding significant motifs in genome sequences, evolutionary motif finding algorithms being one of them. The work presented in this paper uses Differential Evolution (DE) Algorithm to discover new motifs in rice genome sequences and aims to provide an intuitive wizard to analyse the micro-array analysis of expression patterns (motifs) for the queried genes. The used DE algorithm involves crossover operation with fine tuning. Further, to search for already known motifs parallel version of adaptive hash based pattern matching algorithm has been implemented. The study is conducted on rice genome sequences for twelve chromosomes each consisting of approximately 70000 genome sequences. In this paper, experimental results provide a comparison of serial and parallel version of the algorithm applied for the same dataset which shows that parallel implementation improves the performance by almost 25-30% to search the patterns in genome sequences and provide a list of newly discovered significant motifs.

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“…The extended backward oracle matching algorithm [19] was also proposed to handle long patterns and small alphabets. But the memory utilization of these algorithms was huge.…”

Section: Literature Reviewmentioning

confidence: 99%

An Intuitive Wizard to Identify Pattern in Similarity Expressed Gene Set of Rice

Barrow¹,

Naryanan²

2018

IJIES

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“…Faro and Lecroq presented Extended-Backward-Oracle-Matching (EBOM) and Forward-Simplified-Backward-Nondeterministic-DAWG-Matching (FSBNDM) in 2009 [10]. Both are variants of the Backward-Oracle-Matching algorithm and based on finite automata.…”

Section: Variants Of the Backward-oracle-matchingmentioning

confidence: 99%

Parallel String Matching

Pfaffe

Tillmann

Lutteropp

et al. 2017

Euro-Par 2016: Parallel Processing Workshops

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Abstract. We explore the benefits of parallelizing 7 state-of-the-art string matching algorithms. Using SIMD and multi-threading techniques we achieve a significant performance improvement of up to 43.3x over reference implementations and a speedup of up to 16.7x over the string matching program grep. We evaluate our implementations on the smart-corpora and the full human genome data set. We show scalability over number of threads and impact of pattern length.

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“…Among the various improvements of the BNDM algorithm we mention the Simplified BNDM algorithm improved with Horspool shift [9], with q-grams [4,15], and with lookahead characters [6,15]. The BNDM algorithm has been also modified in order to match long patterns [5] and binary strings [7].…”

Section: Multiple Windows Variants Of Bit-parallel Algorithmsmentioning

confidence: 99%

“…7.11 (4) 5.93 (4) 5.48 (4) 5.37 (4) 5.36 (4) 5.36 (4) 5.33 (4) 5.31 (4) TVSBS-W(k) 9.77 (4) 8.13 (4) 6.81 (6) 5.92 (6) 5.48 (6) 5.33 (6) 5.19 (6) 5.06 (6) 4.94 (6) ( 5.45 (6) 5.07 (6) 5.06 (6) 5.10 (6) 5.06 (6) 5.06 (6) 5.05 (6) FSBNDM-W(k) 8.44 (4) 6.28 (2) 5.04…”

Section: 38unclassified

“…This is done by using factor automata, data structures which identify all factors of a word. Among them the Extended Backward Oracle Matching algorithm [6] (EBOM for short) is one of the most efficient algorithms especially for long patterns. Another algorithm based on the bit-parallel simulation [17] of the nondeterministic factor automaton, and called Backward Nondeterministic Dawg Match algorithm [13] (BNDM), is very efficient for short patterns.…”

Section: Introductionmentioning

confidence: 99%

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A Multiple Sliding Windows Approach to Speed Up String Matching Algorithms

Faro

Lecroq

2012

Experimental Algorithms

Self Cite

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Abstract. In this paper we present a general approach to string matching based on multiple sliding text-windows, and show how it can be applied to some among the most efficient algorithms for the problem based on nondeterministic automata and comparison of characters. From our experimental results it turns out that the new multiple sliding windows approach leads to algorithms which obtain better results than the original ones when searching texts over relatively large alphabets. Best improvements are obtained especially for short patterns.

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Efficient Variants of the Backward-Oracle-Matching Algorithm

Cited by 37 publications

References 16 publications

An Intuitive Wizard to Identify Pattern in Similarity Expressed Gene Set of Rice

An Intuitive Wizard to Identify Pattern in Similarity Expressed Gene Set of Rice

Parallel String Matching

A Multiple Sliding Windows Approach to Speed Up String Matching Algorithms

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