Efficient pattern matching in elastic-degenerate strings

Motivated by applications in bioinformatics and image searching, in what follows, we study the classic pattern matching problem in the context of elastic-degenerate strings: the generalised notion of gapped strings. An elastic-degenerate string can be seen as an ordered collection of k strings interleaved by k − 1 elastic-degenerate symbols, where each such elastic-degenerate symbol corresponds to a set of two or more variable-length strings. We present efficient algorithms for two variants of the pattern matching problem on elastic-degenerate strings: first, for a solid pattern and an elastic-degenerate text; second, for an elastic-degenerate pattern and a solid text. A proof-of-concept implementation of the former is provided.

Authors

• Costas S. Iliopoulos
• Ritu Kundu
• Solon P. Pissis

Keywords

• Algorithms on strings
• Degenerate strings
• Indeterminate strings
• Elastic-degenerate strings
• Gapped strings