Approximate Abelian Periods to Find Motifs in Biological Sequences

Mendivelso, Juan; Pino, Camilo; Niño, Luís Fernando; Pinzón, Yoan J.

doi:10.1007/978-3-319-24462-4_11

Cited by 4 publications

(4 citation statements)

References 14 publications

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“…As for this last aspect, parameterized matching has applications in several areas. It was formerly used in software maintenance for code clone detection [24]- [26]; its extensions can be profitably exploited in image processing and computational biology [27]- [29], in music information retrieval [30], and even for solving the graph isomorphism problem [31]. While [2] introduces exact parameterized match, mismatches are studied in [32].…”

Section: Related Workmentioning

confidence: 99%

“…The δγ distance has been designed to compare equal length integer strings; they are said to δγ -match if their corresponding symbols differ at most by δ, and the sum of such differences is at most γ . This metric has found interesting applications in bioinformatics [27] and music information retrieval [30]. In [39], a parameterized version of the δγ distance has been presented.…”

Section: Related Workmentioning

confidence: 99%

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A General Approach to Uniformly Handle Different String Metrics Based on Heterogeneous Alphabets

et al. 2020

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In the last few years, we have assisted in a great increase of the usage of strings in the most disparate areas. In the meantime, the development of the Internet has brought the necessity of managing strings from very different contexts and possibly using different alphabets. This issue is not addressed by the numerous string comparison metrics previously proposed in the literature. In this paper, we aim at providing a contribution in this context. In fact, first we propose an approach to measure the similarity of strings based on different alphabets. Then we show that our approach can be specifically adapted to several classic string comparison metrics and that each specialization can lead to addressing completely different issues.

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Section: Related Workmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

A General Approach to Uniformly Handle Different String Metrics Based on Heterogeneous Alphabets

et al. 2020

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“…Cambouropoulos et al [3] was perhaps the first to mention this problem motivated by Crawford's work et al [6]. Recently, it has been used to make flexible other string matching paradigms such as parameterized matching [20], [21], function matching [22] and jumbled matching [23], [24].…”

Section: Introductionmentioning

confidence: 99%

New Algorithms for δγ-Order Preserving Matching

Mendivelso

Niquefa

Pinzón

et al. 2018

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Context: Order-preserving matching regards the relative order of strings. However, its application areas require more flexibility in the matching paradigm. We advance in this direction in this paper that extends our previous work [27].Method: We define γ -order preserving matching as an approximate variant of order-preserving matching. We devise two solutions for it based on segment and Fenwick trees: segtreeBA and bitBA.Results: We experimentally show the efficiency of our algorithms compared to the ones presented in [26] (naiveA and updateBA). Also, we present applications of our approach in music retrieval and stock market analysis.Conclusions: Even though the worst-case time complexity of the proposed algorithms (namely, O(nm log m)) is higher than the Ѳ(nm)-time complexity of updateBA, their Ω (n log n) lower bound makes them more efficient in practice. On the other hand, we show that our approach is useful to identify similarity in music melodies and stock price trends through real application examples.

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“…Many kinds of algorithms have been put forward to resolve δγ-matching (see for instance Cambouropoulos et al, (2002), Crochemore et al, (2002), Crochemore et al, (2003), Clifford and Iliopoulos (2004), Cantone et al, (2004), Crochemore et al, (2005) and Lee et al, (2006)). Recently, it has been used to make more flexible other string matching paradigms such as parameterized matching (see for instance Lee et al, (2008) and Mendivelso (2010)), function matching (Mendivelso et al, (2012)) and jumbled matching (Mendivelso et al, (2015) and Mendivelso et al, (2014)).…”

Section: Introductionmentioning

confidence: 99%

A novel approach to approximate order preserving matching

et al. 2017

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Un problema importante en el análisis de mercado de valores y la recuperación de información musical es el emparejamiento con preservación de orden. Este problema es una variante recientemente introducida del problema de emparejamiento de cadenas en el que busca subcadenas en el texto cuya representación natural coincide con la representación natural del patrón. La representación natural de una cadena X es una cadena que contiene los rankings de los caracteres que ocurren en cada posición de X. Entonces, el emparejamiento con preservación de orden considera la estructura interna de las cadenas en lugar de sus valores absolutos. Pero tanto en el análisis de mercado de valores como en la recuperación de información musical, se requiere más flexibilidad: no sólo las subcadenas con exactamente la misma estructura son de interés, sino también las que son similares. En este artículo se propone una versión aproximada del problema de emparejamiento con preservación de orden basada en las distancias δγ que permiten un error individual entre el ranking de los símbolos correspondientes (delimitada por δ) y un error global de todas los rankings (delimitadas por γ). Se presenta un algoritmo que resuelve este problema en O(nm+m log m). Los resultados experimentales verifican la eficiencia del algoritmo propuesto.

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Approximate Abelian Periods to Find Motifs in Biological Sequences

Cited by 4 publications

References 14 publications

A General Approach to Uniformly Handle Different String Metrics Based on Heterogeneous Alphabets

A General Approach to Uniformly Handle Different String Metrics Based on Heterogeneous Alphabets

New Algorithms for δγ-Order Preserving Matching

A novel approach to approximate order preserving matching

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