Multi-pattern matching with variable-length wildcards using suffix tree

2018 ◽  
Vol 21 (4) ◽  
pp. 1151-1165 ◽  
Author(s):  
Na Liu ◽  
Fei Xie ◽  
Xindong Wu
Keyword(s):  
Pattern Matching ◽  
Suffix Tree ◽  
Variable Length

Suffix array for multi-pattern matching with variable length wildcards

2021 ◽  
Vol 25 (2) ◽  
pp. 283-303
Author(s):  
Na Liu ◽  
Fei Xie ◽  
Xindong Wu
Keyword(s):  
Dynamic Programming ◽  
Data Structure ◽  
Pattern Matching ◽  
Edit Distance ◽  
State Of The Art ◽  
Suffix Array ◽  
Variable Length ◽  
Distance Method ◽  
Efficient Data ◽  
Comparison Algorithms

Approximate multi-pattern matching is an important issue that is widely and frequently utilized, when the pattern contains variable-length wildcards. In this paper, two suffix array-based algorithms have been proposed to solve this problem. Suffix array is an efficient data structure for exact string matching in existing studies, as well as for approximate pattern matching and multi-pattern matching. An algorithm called MMSA-S is for the short exact characters in a pattern by dynamic programming, while another algorithm called MMSA-L deals with the long exact characters by the edit distance method. Experimental results of Pizza & Chili corpus demonstrate that these two newly proposed algorithms, in most cases, are more time-efficient than the state-of-the-art comparison algorithms.

Practical Variable Length Gap Pattern Matching

2016 ◽  
pp. 1-16 ◽  
Author(s):  
Johannes Bader ◽  
Simon Gog ◽  
Matthias Petri
Keyword(s):  
Pattern Matching ◽  
Variable Length

scholarly journals INDEXING GAPPED-FACTORS USING A TREE

2008 ◽  
Vol 19 (01) ◽  
pp. 71-87 ◽  
Author(s):  
PIERRE PETERLONGO ◽  
JULIEN ALLALI ◽  
MARIE-FRANCE SAGOT
Keyword(s):  
Data Structure ◽  
Pattern Matching ◽  
Suffix Tree ◽  
Linear Time ◽  
Fixed Size ◽  
Specific Kind ◽  
Time And Space ◽  
Inference Problems

We present a data structure to index a specific kind of factors, that is of substrings, called gapped-factors. A gapped-factor is a factor containing a gap that is ignored during the indexation. The data structure presented is based on the suffix tree and indexes all the gapped-factors of a text with a fixed size of gap, and only those. The construction of this data structure is done online in linear time and space. Such a data structure may play an important role in various pattern matching and motif inference problems, for instance in text filtration.

Sign in / Sign up

Export Citation Format

Share Document