An Enumeration Algorithm of Short Hamming Distance Based on Grammar Compression

Abstract

We propose an enumeration algorithm of short Hamming distance based on grammar compression by using split search. Pattern search and frequent pattern discovery using ESP-index[9] have been proposed, but enumeration algorithm of short Hamming distance has not been proposed yet. Using ESP-index and split search, we propose an enumeration algorithm of short Hamming distance. We experiment our algorithm for DNA text and achieve fastar calculate than FM-index[10].