Efficient pattern matching in elastic-degenerate strings

Efficient Pattern Matching in Elastic-Degenerate Strings

In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such that each elastic-degenerate symbol corresponds to a set of two or more variable length strings. Here, we present an algorithm for solving the pattern matchi...

Efficient pattern matching in degenerate strings with the Burrows-Wheeler transform

A degenerate or indeterminate string on an alphabet Σ is a sequence of non-empty subsets of Σ. Given a degenerate string t of length n, we present a new method based on the Burrows–Wheeler transform for searching for a degenerate pattern of length m in t running in O(mn) time on a constant size alphabet Σ. Furthermore, it is a hybrid patternmatching technique that works on both regular and dege...

Efficient Pattern Matching on Binary Strings

The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in telecom and computer network applications. Moreover the problem finds applications also in the field of image processing and in pattern matching on compressed ...

Pattern Matching in Strings

Unique Pattern Matching in Strings

Regular expression patterns are a key feature of document processing languages like Perl and XDuce. It is in this context that the first and longest match policies have been proposed to disambiguate the pattern matching process. We formally define a matching semantics with these policies and show that the generally accepted method of simulating longest match by first match and recursion is inco...