The k-mappability problem revisited

Amihood Amir; Itai Boneh; Eitan Kondratovsky

doi:10.4230/LIPIcs.CPM.2021.5

The k-mappability problem revisited

Amihood Amir, Itai Boneh, Eitan Kondratovsky

Department of Computer Science

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

1 Scopus citations

Abstract

The k-mappability problem has two integers parameters m and k. For every subword of size m in a text S, we wish to report the number of indices in S in which the word occurs with at most k mismatches. The problem was lately tackled by Alzamel et al. [1]. For a text with constant alphabet S and k ϵ O(1), they present an algorithm with linear space and O(n logk+1 n) time. For the case in which k = 1 and a constant size alphabet, a faster algorithm with linear space and O(n log(n) log log(n)) time was presented in [2]. In this work, we enhance the techniques of [2] to obtain an algorithm with linear space and O(n log(n)) time for k = 1. Our algorithm removes the constraint of the alphabet being of constant size. We also present linear algorithms for the case of k = 1, |S| ϵ O(1) and m =Ω(√n).

Original language	English
Title of host publication	32nd Annual Symposium on Combinatorial Pattern Matching, CPM 2021
Editors	Pawel Gawrychowski, Tatiana Starikovskaya
Publisher	Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)	9783959771863
DOIs	https://doi.org/10.4230/LIPIcs.CPM.2021.5
State	Published - 1 Jul 2021
Event	32nd Annual Symposium on Combinatorial Pattern Matching, CPM 2021 - Wroclaw, Poland Duration: 5 Jul 2021 → 7 Jul 2021

Publication series

Name	Leibniz International Proceedings in Informatics, LIPIcs
Volume	191
ISSN (Print)	1868-8969

Conference

Conference	32nd Annual Symposium on Combinatorial Pattern Matching, CPM 2021
Country/Territory	Poland
City	Wroclaw
Period	5/07/21 → 7/07/21

Bibliographical note

Publisher Copyright:
© Amihood Amir, Itai Boneh, and Eitan Kondratovsky.

Funding

Funding Amihood Amir: Partly supported by ISF grant 1475/18, BSF grant 2018141 and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No 683064. Itai Boneh: Partly supported by ISF grant 1475/75. Eitan Kondratovsky: Partly supported by ISF grant 1475/18. Amihood Amir: Partly supported by ISF grant 1475/18, BSF grant 2018141 and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme grant agreement No 683064 Partly supported by ISF grant 1475/75. Partly supported by ISF grant 1475/18.

Funders	Funder number
Horizon 2020 Framework Programme	1475/75, 683064
European Commission
European Commission
United States-Israel Binational Science Foundation	2018141
Israel Science Foundation	1475/18

Keywords

Hamming Distance
Pattern Matching
Suffix Array
Suffix Tree

Access to Document

10.4230/LIPIcs.CPM.2021.5

Cite this

Amir, A., Boneh, I., & Kondratovsky, E. (2021). The k-mappability problem revisited. In P. Gawrychowski, & T. Starikovskaya (Eds.), 32nd Annual Symposium on Combinatorial Pattern Matching, CPM 2021 Article 5 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 191). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.CPM.2021.5

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Amir, A, Boneh, I & Kondratovsky, E 2021, The k-mappability problem revisited. in P Gawrychowski & T Starikovskaya (eds), 32nd Annual Symposium on Combinatorial Pattern Matching, CPM 2021., 5, Leibniz International Proceedings in Informatics, LIPIcs, vol. 191, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 32nd Annual Symposium on Combinatorial Pattern Matching, CPM 2021, Wroclaw, Poland, 5/07/21. https://doi.org/10.4230/LIPIcs.CPM.2021.5

The k-mappability problem revisited. / Amir, Amihood; Boneh, Itai; Kondratovsky, Eitan.
32nd Annual Symposium on Combinatorial Pattern Matching, CPM 2021. ed. / Pawel Gawrychowski; Tatiana Starikovskaya. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2021. 5 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 191).

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

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The k-mappability problem revisited

Abstract

Publication series

Conference

Bibliographical note

Funding

Keywords

Access to Document

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Cite this