Linear Algorithm for Conservative Degenerate Pattern Matching

TL;DR

This paper introduces the first linear-time algorithm for matching conservative degenerate strings with a fixed number of non-solid symbols, improving efficiency in pattern matching tasks involving such strings.

Contribution

It presents a novel linear-time algorithm for conservative degenerate pattern matching, handling strings with a bounded number of non-solid symbols.

Findings

Algorithm operates in O(nk) time for strings with k non-solid symbols.

First linear-time solution for conservative degenerate string matching.

Efficiently finds all occurrences of a pattern in a text with degenerate symbols.

Abstract

A degenerate symbol x* over an alphabet A is a non-empty subset of A, and a sequence of such symbols is a degenerate string. A degenerate string is said to be conservative if its number of non-solid symbols is upper-bounded by a fixed positive constant k. We consider here the matching problem of conservative degenerate strings and present the first linear-time algorithm that can find, for given degenerate strings P* and T* of total length n containing k non-solid symbols in total, the occurrences of P* in T* in O(nk) time.