TY - GEN

T1 - r-Indexing the eBWT

AU - Sciortino, Marinella

AU - Boucher, Christina

AU - Lipták, Zsuzsanna

AU - Rossi, Massimiliano

AU - Cenzato, Davide

PY - 2021

Y1 - 2021

N2 - The extended Burrows Wheeler Transform (eBWT ) was introduced by Mantaci et al. [TCS 2007] to extend the definition of the BWT to a collection of strings. In our prior work [SPIRE 2021], we give a linear-time algorithm for the 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 eBWT, i.e., run-length encoded eBWT and 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 eBWT can be efficiently supported.

AB - The extended Burrows Wheeler Transform (eBWT ) was introduced by Mantaci et al. [TCS 2007] to extend the definition of the BWT to a collection of strings. In our prior work [SPIRE 2021], we give a linear-time algorithm for the 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 eBWT, i.e., run-length encoded eBWT and 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 eBWT can be efficiently supported.

UR - http://hdl.handle.net/10447/526397

M3 - Conference contribution

SN - 978-3-030-86691-4; 978-3-030-86692-1

T3 - LECTURE NOTES IN ARTIFICIAL INTELLIGENCE

SP - 3

EP - 12

BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

ER -