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 -