An Efficient Matching Algorithm for Encoded DNA Sequences and Binary Strings

We present a new efficient algorithm for exact matching in encoded DNA sequences and on binary strings. Our algorithm combines a multi-pattern version of the Bndm algorithm and a simplified version of the Commentz-Walter algorithm. We performed also experimental comparisons with the most efficient algorithms presented in the literature. Experimental results show that the newly presented algorithm outperforms existing solutions in most cases.

• Type: Conference
• Year: 2009
• Where: CPM
• Authors: Simone Faro, Thierry Lecroq
• Keywords: Algorithm, Bndm Algorithm, Combinatorics, CPM 2009, Efficient Algorithms