### Abstract

Motivation: A palindrome is a string that reads the same forward and backward. Finding palindromic substructures is important in DNA, RNA or protein sequence analysis. We say that two strings of the same length are pal-equivalent if, for each possible centre, they have the same length of the maximal palindrome. Given a text T of length n and a pattern P of length m, we study the palindrome pattern matching problem that finds all indices i such that P and T[i-m+1:i] are pal-equivalent. Results: We first solve the online palindrome pattern matching problem in O(m^{2}) preprocessing time and O(mn) query time using O(m^{2}) space. We then extend the problem for multiple patterns and solve the online multiple palindrome pattern matching problem in O(mkM) preprocessing time and O(mkn+c) query time using O(mkM) space, where M is the sum of all pattern lengths, m_{k} is the longest pattern length and c is the number of pattern occurrences.

Original language | English |
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Pages (from-to) | 1151-1157 |

Number of pages | 7 |

Journal | Bioinformatics |

Volume | 32 |

Issue number | 8 |

DOIs | |

Publication status | Published - 2016 Apr 15 |

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### All Science Journal Classification (ASJC) codes

- Statistics and Probability
- Medicine(all)
- Biochemistry
- Molecular Biology
- Computer Science Applications
- Computational Theory and Mathematics
- Computational Mathematics

### Cite this

*Bioinformatics*,

*32*(8), 1151-1157. https://doi.org/10.1093/bioinformatics/btv738

}

*Bioinformatics*, vol. 32, no. 8, pp. 1151-1157. https://doi.org/10.1093/bioinformatics/btv738

**OMPPM : Online multiple palindrome pattern matching.** / Kim, Hwee; Han, Yo-Sub.

Research output: Contribution to journal › Article

TY - JOUR

T1 - OMPPM

T2 - Online multiple palindrome pattern matching

AU - Kim, Hwee

AU - Han, Yo-Sub

PY - 2016/4/15

Y1 - 2016/4/15

N2 - Motivation: A palindrome is a string that reads the same forward and backward. Finding palindromic substructures is important in DNA, RNA or protein sequence analysis. We say that two strings of the same length are pal-equivalent if, for each possible centre, they have the same length of the maximal palindrome. Given a text T of length n and a pattern P of length m, we study the palindrome pattern matching problem that finds all indices i such that P and T[i-m+1:i] are pal-equivalent. Results: We first solve the online palindrome pattern matching problem in O(m2) preprocessing time and O(mn) query time using O(m2) space. We then extend the problem for multiple patterns and solve the online multiple palindrome pattern matching problem in O(mkM) preprocessing time and O(mkn+c) query time using O(mkM) space, where M is the sum of all pattern lengths, mk is the longest pattern length and c is the number of pattern occurrences.

AB - Motivation: A palindrome is a string that reads the same forward and backward. Finding palindromic substructures is important in DNA, RNA or protein sequence analysis. We say that two strings of the same length are pal-equivalent if, for each possible centre, they have the same length of the maximal palindrome. Given a text T of length n and a pattern P of length m, we study the palindrome pattern matching problem that finds all indices i such that P and T[i-m+1:i] are pal-equivalent. Results: We first solve the online palindrome pattern matching problem in O(m2) preprocessing time and O(mn) query time using O(m2) space. We then extend the problem for multiple patterns and solve the online multiple palindrome pattern matching problem in O(mkM) preprocessing time and O(mkn+c) query time using O(mkM) space, where M is the sum of all pattern lengths, mk is the longest pattern length and c is the number of pattern occurrences.

UR - http://www.scopus.com/inward/record.url?scp=84966602683&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84966602683&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btv738

DO - 10.1093/bioinformatics/btv738

M3 - Article

VL - 32

SP - 1151

EP - 1157

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 8

ER -