2015/06/15 by Maxime Crochemore, Costas S. Iliopoulos, Crochemore, Maxime +7
Biochemistry, Genetics and Molecular Biology · Computer Science · #Algorithms and Data Compression #DNA and Biological Computing #Data Structures and Algorithms (cs.DS) #FOS: Computer and information sciences #semigroups and automata theory
paper · pdf · doi:10.48550/arxiv.1506.04559
openalex publication_date 2015/06/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.