String matching with lookahead

Abstract

Forward-SBNDM is a recently introduced variation of the BNDM algorithm for exact string matching. Forward-SBNDM inspects a 2-gram in the text such that the first character is the last one of an alignment window of the pattern and the second one is then outside the window. We present a generalization of this idea by inspecting several lookahead characters beyond an alignment window and integrate it with SBNDMq, a q-gram variation of BNDM. As a result, we get several new variations of SBNDMq. In addition, we introduce a greedy skip loop for SBNDM2. We tune up our algorithms and the reference algorithms with 2-byte read. According to our experiments, the best of the new variations are faster than the winners of recent algorithm comparisons for English, DNA, and binary data.