String matching with variable length gaps

String Matching with Variable Length Gaps

We consider string matching with variable length gaps. Given a string T and a pattern P consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending positions of substrings in T that match P . This problem is a basic primitive in computational biology applications. Let m and n be the lengths of P and T , respective...

Online Dictionary Matching with Variable-Length Gaps

Approximate String Matching with Gaps

In this paper we consider several new versions of approximate string matching with gaps. The main characteristic of these new versions is the existence of gaps in the matching of a given pattern in a text. Algorithms are sketched for each version and their time and space complexity is stated. The specific versions of approximate string matching have various applications in computerized music an...

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 oft...

Finding Patterns with Variable Length Gaps or Don't Cares

In this paper we have presented new algorithms to handle the pattern matching problem where the pattern can contain variable length gaps. Given a pattern P with variable length gaps and a text T our algorithm works in O(n + m + α log(max1<=i<=l(bi − ai))) time where n is the length of the text, m is the summation of the lengths of the component subpatterns, α is the total number of occurrences ...