Large-scale pattern search using reduced-space on-disk suffix arrays

Abstract

The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix pointers. In this paper, we describe a new two-level suffix array-based index structure that requires significantly less disk space than previous approaches. Key to the saving is the use of disk blocks that are based on prefixes rather than the more usual uniform-sampling approach, allowing reductions between blocks and subparts of other blocks. We also describe a new in-memory structure-the condensed BWT-and show that it allows common patterns to be resolved..