A constant-space comparison-based algorithm for computing the Burrows-Wheeler transform

Maxime Crochemore; Roberto Grossi; Juha Kärkkäinen; Gad M. Landau

doi:10.1007/978-3-642-38905-4_9

A constant-space comparison-based algorithm for computing the Burrows-Wheeler transform

Maxime Crochemore, Roberto Grossi, Juha Kärkkäinen, Gad M. Landau

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

We introduce the problem of computing the Burrows- Wheeler Transform (BWT) using just O(1) additional space. Our in-place algorithm does not need the explicit storage for the suffix sort array and the output array, as typically required in previous work. It relies on the combinatorial properties of the BWT, and runs in O(n²) time in the comparison model using O(1) extra memory cells, apart from the array of n cells storing the n characters of the input text. We also discuss some time-space trade-offs for the inverse algorithm to obtain the text from the given BWT. \ 2013 Springer-Verlag.

Original language	English
Title of host publication	Combinatorial Pattern Matching - 24th Annual Symposium, CPM 2013, Proceedings
Pages	74-82
Number of pages	9
DOIs	https://doi.org/10.1007/978-3-642-38905-4_9
State	Published - 2013
Event	24th Annual Symposium on Combinatorial Pattern Matching, CPM 2013 - Bad Herrenalb, Germany Duration: 17 Jun 2013 → 19 Jun 2013

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	7922 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	24th Annual Symposium on Combinatorial Pattern Matching, CPM 2013
Country/Territory	Germany
City	Bad Herrenalb
Period	17/06/13 → 19/06/13

Bibliographical note

Funding Information:
The work of the third author has been supported by the Academy of Finland grant 118653 (ALGODAN). The work of the fourth author has been partially supported by the National Science Foundation Award 0904246, Israel Science Foundation grant 347/09, Yahoo, Grant No. 2008217 from the United States-Israel Binational Science Foundation (BSF) and DFG.

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-642-38905-4_9

Cite this

Crochemore, M., Grossi, R., Kärkkäinen, J., & Landau, G. M. (2013). A constant-space comparison-based algorithm for computing the Burrows-Wheeler transform. In Combinatorial Pattern Matching - 24th Annual Symposium, CPM 2013, Proceedings (pp. 74-82). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7922 LNCS). https://doi.org/10.1007/978-3-642-38905-4_9

Crochemore, Maxime ; Grossi, Roberto ; Kärkkäinen, Juha et al. / A constant-space comparison-based algorithm for computing the Burrows-Wheeler transform. Combinatorial Pattern Matching - 24th Annual Symposium, CPM 2013, Proceedings. 2013. pp. 74-82 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "We introduce the problem of computing the Burrows- Wheeler Transform (BWT) using just O(1) additional space. Our in-place algorithm does not need the explicit storage for the suffix sort array and the output array, as typically required in previous work. It relies on the combinatorial properties of the BWT, and runs in O(n2) time in the comparison model using O(1) extra memory cells, apart from the array of n cells storing the n characters of the input text. We also discuss some time-space trade-offs for the inverse algorithm to obtain the text from the given BWT. \ 2013 Springer-Verlag.",

author = "Maxime Crochemore and Roberto Grossi and Juha K{\"a}rkk{\"a}inen and Landau, {Gad M.}",

note = "Funding Information: The work of the third author has been supported by the Academy of Finland grant 118653 (ALGODAN). The work of the fourth author has been partially supported by the National Science Foundation Award 0904246, Israel Science Foundation grant 347/09, Yahoo, Grant No. 2008217 from the United States-Israel Binational Science Foundation (BSF) and DFG.; 24th Annual Symposium on Combinatorial Pattern Matching, CPM 2013 ; Conference date: 17-06-2013 Through 19-06-2013",

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Crochemore, M, Grossi, R, Kärkkäinen, J & Landau, GM 2013, A constant-space comparison-based algorithm for computing the Burrows-Wheeler transform. in Combinatorial Pattern Matching - 24th Annual Symposium, CPM 2013, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7922 LNCS, pp. 74-82, 24th Annual Symposium on Combinatorial Pattern Matching, CPM 2013, Bad Herrenalb, Germany, 17/06/13. https://doi.org/10.1007/978-3-642-38905-4_9

A constant-space comparison-based algorithm for computing the Burrows-Wheeler transform. / Crochemore, Maxime; Grossi, Roberto; Kärkkäinen, Juha et al.
Combinatorial Pattern Matching - 24th Annual Symposium, CPM 2013, Proceedings. 2013. p. 74-82 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7922 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Crochemore M, Grossi R, Kärkkäinen J, Landau GM. A constant-space comparison-based algorithm for computing the Burrows-Wheeler transform. In Combinatorial Pattern Matching - 24th Annual Symposium, CPM 2013, Proceedings. 2013. p. 74-82. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-38905-4_9

A constant-space comparison-based algorithm for computing the Burrows-Wheeler transform

Abstract

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Bibliographical note

ASJC Scopus subject areas

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