Finding All Approximate Gapped Palindromes

Hsu, Ping-Hui; Chen, Kuan‐Yu; Chao, Kun-Mao

doi:10.1142/s0129054110007647

Cited by 14 publications

(13 citation statements)

References 13 publications

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“…The main idea in both [13] and [11] is the efficient computation of the so-called h-waves. In the standard dynamic programming matrix for two strings x and y, we say that a cell…”

Section: Verification Schemementioning

confidence: 99%

Average-Case Optimal Approximate Circular String Matching

Barton

Iliopoulos

Pissis

2015

Language and Automata Theory and Applications

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Abstract. Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that are at a distance at most k from x or from any of its rotations. In this article, we present a new algorithm for approximate circular string matching under the edit distance model with optimal average-case search time O(n(k + log m)/m). Optimal averagecase search time can also be achieved by the algorithms for multiple approximate string matching (Fredriksson and Navarro, 2004) using x and its rotations as the set of multiple patterns. Here we reduce the preprocessing time and space requirements compared to that approach.

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“…The main idea in both [13] and [11] is the efficient computation of the so-called h-waves. In the standard dynamic programming matrix for two strings x and y, we say that a cell…”

Section: Verification Schemementioning

confidence: 99%

Average-Case Optimal Approximate Circular String Matching

Barton

Iliopoulos

Pissis

2015

Language and Automata Theory and Applications

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“…[14]. Several problems were considered such as, enumeration of exact gapped palindromes of a string [10] and also enumeration of approximate gapped palindromes [7,13], finding maximal length of long armed or and constrained length gapped palindrome [5].…”

Section: Introductionmentioning

confidence: 99%

Block Palindromes: A New Generalization of Palindromes

Goto

Tomohiro

Bannai

et al. 2018

String Processing and Information Retrieval

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We study a new generalization of palindromes and gapped palindromes called block palindromes. A block palindrome is a string that becomes a palindrome when identical substrings are replaced with a distinct character. We investigate several properties of block palindromes and in particular, study substrings of a string which are block palindromes. In so doing, we introduce the notion of a maximal block palindrome, which leads to a compact representation of all block palindromes that occur in a string. We also propose an algorithm which enumerates all maximal block palindromes that appear in a given string T in O(|T | + MBP (T ) ) time, where MBP (T ) is the output size, which is optimal unless all the maximal block palindromes can be represented in a more compact way.

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“…We present an equally efficient approach for computing all maximal palindromes under the edit distance. After our conference publication [1], we have learnt about alternative algorithms computing this type of maximal approximate palindromes [22,16]. The approach of [22] works in O(n · δ 2 ) time.…”

Section: Introductionmentioning

confidence: 99%

Palindromic Decompositions with Gaps and Errors

Adamczyk

Alzamel

Charalampopoulos

et al. 2017

Computer Science – Theory and Applications

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Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient algorithms for the factorization of sequences into palindromes and maximal palindromes have been devised in recent years. We extend these studies by allowing gaps in decompositions and errors in palindromes, and also imposing a lower bound to the length of acceptable palindromes.We first present an algorithm for obtaining a palindromic decomposition of a string of length n with the minimal total gap length in time O(n log n · g) and space O(n · g), where g is the number of allowed gaps in the decomposition. We then consider a decomposition of the string in maximal δ-palindromes (i.e. palindromes with δ errors under the edit or Hamming distance) and g allowed gaps. We present an algorithm to obtain such a decomposition with the minimal total gap length in time O(n · (g + δ)) and space O(n · g).

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Finding All Approximate Gapped Palindromes

Cited by 14 publications

References 13 publications

Average-Case Optimal Approximate Circular String Matching

Average-Case Optimal Approximate Circular String Matching

Block Palindromes: A New Generalization of Palindromes

Palindromic Decompositions with Gaps and Errors

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