6533b7d9fe1ef96bd126d752
RESEARCH PRODUCT
r-Indexing the eBWT
Zsuzsanna LiptákMassimiliano RossiChristina BoucherMarinella SciortinoDavide Cenzatosubject
Physicsstring compressionBurrows–Wheeler transformSettore INF/01 - InformaticaSearch engine indexingSuffix arrayOrder (ring theory)Burrows-Wheeler-Transform r-index string compression extended BWT compressed indexingBurrows-Wheeler-Transformlaw.inventionCombinatoricsr-indexcompressed indexinglawIndexingextended BWTdescription
The extended Burrows Wheeler Transform (\(\mathrm {eBWT}\)) was introduced by Mantaci et al. [TCS 2007] to extend the definition of the \(\mathrm {BWT}\) to a collection of strings. In our prior work [SPIRE 2021], we give a linear-time algorithm for the \(\mathrm {eBWT}\) that preserves the fundamental property of the original definition (i.e., the independence from the input order). The algorithm combines a modification of the Suffix Array Induced Sorting (SAIS) algorithm [IEEE Trans Comput 2011] with Prefix Free Parsing [AMB 2019; JCB 2020]. In this paper, we show how this construction algorithm leads to r-indexing the \(\mathrm {eBWT}\), i.e., run-length encoded \(\mathrm {eBWT}\) and \(\mathrm {SA}\) samples of Gagie et al. [SODA 2018] can be constructed efficiently from the components of the PFP. Moreover, we show that finding maximal exact matches (MEMs) between a query string and the r-index of the \(\mathrm {eBWT}\) can be efficiently supported.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2021-01-01 |