TY - GEN
T1 - Computing the Parameterized Burrows–Wheeler Transform Online
AU - Hashimoto, Daiki
AU - Hendrian, Diptarama
AU - Köppl, Dominik
AU - Yoshinaka, Ryo
AU - Shinohara, Ayumi
N1 - Funding Information:
Acknowledgments. This work was supported by JSPS KAKENHI Grant Numbers JP19K20208 (DH), JP21K17701 (DK), JP21H05847 (DK), JP22H03551 (DK), JP18H04091 (RY), JP18K11150 (RY), JP20H05703 (RY), and JP21K11745 (AS).
Publisher Copyright:
© 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.
PY - 2022
Y1 - 2022
N2 - Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters. Two parameterized strings are a parameterized match if there is a bijection over all characters such that the bijection transforms one string to the other while keeping the static characters (i.e., it behaves as the identity on the static alphabet). Ganguly et al. [SODA 2017] proposed the parameterized Burrows–Wheeler transform (pBWT) as a variant of the Burrows–Wheeler transform for space-efficient parameterized pattern matching. In this paper, we propose an algorithm for computing the pBWT online by reading the characters of a given input string one-by-one from right to left. Our algorithm works in O(| Π| log n/ log log n) amortized time for each input character, where n and Π denote the size of the input string and the alphabet of the parameter characters, respectively.
AB - Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters. Two parameterized strings are a parameterized match if there is a bijection over all characters such that the bijection transforms one string to the other while keeping the static characters (i.e., it behaves as the identity on the static alphabet). Ganguly et al. [SODA 2017] proposed the parameterized Burrows–Wheeler transform (pBWT) as a variant of the Burrows–Wheeler transform for space-efficient parameterized pattern matching. In this paper, we propose an algorithm for computing the pBWT online by reading the characters of a given input string one-by-one from right to left. Our algorithm works in O(| Π| log n/ log log n) amortized time for each input character, where n and Π denote the size of the input string and the alphabet of the parameter characters, respectively.
KW - Burrows–Wheeler transform
KW - Online algorithm
KW - Parameterized string
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U2 - 10.1007/978-3-031-20643-6_6
DO - 10.1007/978-3-031-20643-6_6
M3 - Conference contribution
AN - SCOPUS:85142749422
SN - 9783031206429
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 70
EP - 85
BT - String Processing and Information Retrieval - 29th International Symposium, SPIRE 2022, Proceedings
A2 - Arroyuelo, Diego
A2 - Arroyuelo, Diego
A2 - Poblete, Barbara
PB - Springer Science and Business Media Deutschland GmbH
T2 - 29th International Symposium on String Processing and Information Retrieval, SPIRE 2022
Y2 - 8 November 2022 through 10 November 2022
ER -