Finding All Approximate Gapped Palindromes

Authors:
Ping-Hui Hsu;Kuan-Yu Chen;Kun-Mao Chao
Affiliations:
Department of Computer Science and Information Engineering,;Department of Computer Science and Information Engineering,;Department of Computer Science and Information Engineering, and Graduate Institute of Biomedical Electronics and Bioinformatics, and Graduate Institute of Networking and Multimedia, National Tai ...
Venue:
ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
Year:
2009

Citing 10
Cited 5

Algorithms for approximate string matching

Information and Control
On finding lowest common ancestors: simplification and parallelization

SIAM Journal on Computing
Algorithms on strings, trees, and sequences: computer science and computational biology

Algorithms on strings, trees, and sequences: computer science and computational biology
Incremental String Comparison

SIAM Journal on Computing
A Dynamic Edit Distance Table

COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Occurrences of palindromes in characteristic Sturmian words

Theoretical Computer Science
Note: Palindrome positions in ternary square-free words

Theoretical Computer Science
Searching for Gapped Palindromes

CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Sequence Comparison: Theory and Methods

Sequence Comparison: Theory and Methods
Efficient algorithms to compute compressed longest common substrings and compressed palindromes

Theoretical Computer Science

Counting and verifying maximal palindromes

SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
Palindrome pattern matching

CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Hardness of longest common subsequence for sequences with bounded run-lengths

CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
Palindrome pattern matching

Theoretical Computer Science
On palindromic sequence automata and applications

CIAA'13 Proceedings of the 18th international conference on Implementation and Application of Automata

Quantified Score

Hi-index	0.00

Visualization

Abstract

We study the problem of finding all maximal approximate gapped palindromes in a string. More specifically, given a string S of length n, a parameter q 驴 0 and a threshold k 0, the problem is to identify all substrings in S of the form uvw such that (1) the Levenshtein distance between u and w r is at most k, where w r is the reverse of w and (2) v is a string of length q. The best previous work requires O(k 2 n) time. In this paper, we propose an O(kn)-time algorithm for this problem by utilizing an incremental string comparison technique. It turns out that the core technique actually solves a more general incremental string comparison problem that allows the insertion, deletion, and substitution of multiple symbols.