Alignment with non-overlapping inversions and translocations on two strings

Cho, Da-Jung; Han, Yo-Sub; Kim, Hwee

doi:10.1016/j.tcs.2014.10.036

Cited by 9 publications

(4 citation statements)

References 8 publications

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“…Regarding the alignment problem with translocations, Cho et al [13] presented a first solution for the case of inversions and translocations of equal length factors (i.e., balanced translocations), working in O(n 3 )-time and O(m 2 )-space. However their solution generalizes the problem to the case where edit operations Authors Year W.C. Time AVG Time Space Alignment with inversions Schoniger and Waterman [26] (1992) O(n 2 m 2 ) -O(m 2 ) Gao et al [19] (2003) O(n 2 m 2 ) -O(nm) Chen et al [12] (2004) O(n 2 m 2 ) -O(nm) Alves et al [5] (2005) O(n 3 log n) -O(n 2 ) Vellozo et al [27] (2006) O(nm 2 ) -O(nm) Alignment with inversions and balanced translocations on both strings Cho et al [13] (2015) O(m 3 ) -O(m 2 ) Pattern matching with inversions Cantone et al [6] (2011) O(nm) -O(m 2 ) Cantone et al [7] (2013) O(nm) O(n) O(m 2 ) Pattern matching with unbalanced translocations Faro and Pavone [18] (2019) O(m 2 ) O(n) O(m) Pattern matching with inversions and balanced translocations Cantone et al [8] (2010) O(nm 2 ) O(n log m) O(m 2 ) Grabowski et al [20] (2011) O(nm 2 ) O(n) O(m) Cantone et al [9] ( Table 1. Results related to alignment and matching of strings allowing for inversions and translocations of factors.…”

Section: Related Resultsmentioning

confidence: 99%

“…Both distances assume that changes between strings occur locally, i.e., only a small portion of the string is involved in the mutation event. However evidence shows that in many applications there are several circumstances where large scale changes are possible [13,15,27]. For instance, such mutations are crucial in dna since they often cause genetic diseases [22,23].…”

Section: Introductionmentioning

confidence: 99%

“…For instance, such mutations are crucial in dna since they often cause genetic diseases [22,23]. For example, large pieces of dna can be moved from one location to another (translocations) [13,25,28,29], or replaced by their reversed complements (inversions) [7].…”

Section: Introductionmentioning

confidence: 99%

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Text Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations

Cantone,

Faro,

Pavone

2021

Preprint

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In this paper we investigate the approximate string matching problem when the allowed edit operations are non-overlapping unbalanced translocations of adjacent factors. Such kind of edit operations take place when two adjacent sub-strings of the text swap, resulting in a modified string. The two involved substrings are allowed to be of different lengths. Such large-scale modifications on strings have various applications. They are among the most frequent chromosomal alterations, accounted for 30% of all losses of heterozygosity, a major genetic event causing inactivation of cancer suppressor genes. In addition, among other applications, they are frequent modifications accounted in musical or in natural language information retrieval. However, despite of their central role in so many fields of text processing, little attention has been devoted to the problem of matching strings allowing for this kind of edit operation. In this paper we present three algorithms for solving the problem, all of them with a O(nm 3 ) worst-case and a O(m 2 )-space complexity, where m and n are the length of the pattern and of the text, respectively. In particular, our first algorithm is based on the dynamic-programming approach. Our second solution improves the previous one by making use of the Directed Acyclic Word Graph of the pattern. Finally our third algorithm is based on an alignment procedure. We also show that under the assumptions of equiprobability and independence of characters, our second algorithm has a O(n log 2 σ m) average time complexity, for an alphabet of size σ ≥ 4.

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Section: Related Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Text Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations

Cantone,

Faro,

Pavone

2021

Preprint

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“…The latter can still be solved in linear time using the suffix tree and admits a number of efficient solutions based on practical approaches [4,9,16,20,25,28], also in the approximate variant [6,7,17,19], as well as an indexing variants [3,20,21], and the problem of detecting various circular patterns [26]. The LCCF problem is further related to the notion of unbalanced translocations [8,10,27,29,30].…”

Section: Introductionmentioning

confidence: 99%