Approximate String Matching with Variable Length Don ' t Care

Searching for DNA or amino acid sequences similar to a given pattern string is very important in molecular biology. In fact, a lot of programs and algorithms have been developed. Most of them are based on alignment of strings or approximate string matching. However, they do not seem to be adequate in some cases. For example, the DNA pattern TATA (known as TATA box) is a common promoter that often appears after the pattern CAATCT (known as CAAT box) within 30 to 50 spaces [3], [6]. To nd strings containing such a pattern, string matching with variable length don't cares is required, where a variable length don't care character can match any substring whose length is in a speci ed range. Moreover, exact matching is not su cient but approximate string matching is required, since the patterns can appear with some probability of error. Thus this paper studies the problem of approximate string matching with variable length don't cares. Here, we brie y review the previous work. Exact string matching with don't cares was studied by Fisher and Paterson [4]. A lot of studies have been done for approximate string matching [5]. Myers and Miller studied approximate string matching of regular expressions [7], and Zhang, Shasha and Wang studied approximate tree matching with variable length don't cares [8]. Although these two studies are close to our problem, the ranges of lengths of don't cares can not be speci ed. Exact string matching with variable length don't cares was studied by Manber and Baeza-Yates [6]. In their work, the range can be speci ed, but approximate matching was not considered. We also developed an algorithm for approximate string matching with don't cares [1]. However, variable length don't cares can not be treated.