Improved algorithm for pattern matching with independent wildcard gaps

Abstract

Pattern matching is critical in some applications such as biological sequence analysis and text filtering. A wildcard gap matches any subsequence with a length in a specified interval, and introduces much adaptability to patterns. However, most existing works require that gaps in a pattern be identical. In this paper, we define a new pattern matching problem where gaps are independently specified. We develop an efficient algorithm to compute the number of all matches based on pattern decomposed. Experimental results show that our algorithm has better performance in the aspects of time complexity and space complexity.