FM-Indexing Grammars Induced by Suffix Sorting for Long Patterns [article]

Jin Jie Deng and Wing-Kai Hon and Dominik Köppl and Kunihiko Sadakane
2021 arXiv   pre-print
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological sequences. Compared to grammar indexes, the size of the RLBWT is often much bigger, but queries like counting the occurrences of long patterns can be done much faster than on any existing grammar index so far. In this paper, we combine the virtues of a grammar with
more » ... he RLBWT by building the RLBWT on top of a special grammar based on induced suffix sorting. Our experiments reveal that our hybrid approach outperforms the classic RLBWT with respect to the index sizes, and with respect to query times on biological data sets for sufficiently long patterns.
arXiv:2110.01181v1 fatcat:7dqamlf5jrgrro56vckacwnwki