A Fast Algorithm for Approximate String Matching on Gene Sequences

Abstract. Approximate string matching is a fundamental and challenging problem in computer science, for which a fast algorithm is highly demanded in many applications including text processing and DNA sequence analysis. In this paper, we present a fast algorithm for approximate string matching, called FAAST. It aims at solving a popular variant of the approximate string matching problem, the k-mismatch problem, whose objective is to find all occurrences of a short pattern in a long text string with at most k mismatches. FAAST generalizes the well-known Tarhio-Ukkonen algorithm by requiring two or more matches when calculating shift distances, which makes the approximate string matching process significantly faster than the Tarhio-Ukkonen algorithm. Theoretically, we prove that FAAST on average skips more characters than the Tarhio-Ukkonen algorithm in a single shift, and makes fewer character comparisons in an entire matching process. Experiments on both simulated data sets and real ...

• Type: Conference
• Year: 2005
• Where: CPM
• Authors: Zheng Liu, Xin Chen, James Borneman, Tao Jiang
• Keywords: Approximate String Matching, CPM 2005, Fast Algorithm, Tarhio-Ukkonen Algorithm