Approximate Hashing for Bioinformatics

Guy Arbitman; Shmuel T. Klein; Pierre Peterlongo; Dana Shapira

doi:10.1007/978-3-030-79121-6_15

Approximate Hashing for Bioinformatics

Guy Arbitman, Shmuel T. Klein, Pierre Peterlongo, Dana Shapira

Department of Computer Science

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

Abstract

The paper extends ideas from data compression by deduplication to the Bioinformatic field. The specific problems on which we show our approach to be useful are the clustering of a large set of DNA strings and the search for approximate matches of long substrings, both based on the design of what we call an approximate hashing function. The outcome of the new procedure is very similar to the clustering and search results obtained by accurate tools, but in much less time and with less required memory.

Original language	English
Title of host publication	Implementation and Application of Automata - 25th International Conference, CIAA 2021, Proceedings
Editors	Sebastian Maneth
Publisher	Springer Science and Business Media Deutschland GmbH
Pages	178-189
Number of pages	12
ISBN (Print)	9783030791209
DOIs	https://doi.org/10.1007/978-3-030-79121-6_15
State	Published - 2021
Event	25th International Conference on Implementation and Application of Automata, CIAA 2021 - Virtual, Online Duration: 19 Jul 2021 → 22 Jul 2021

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	12803 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	25th International Conference on Implementation and Application of Automata, CIAA 2021
City	Virtual, Online
Period	19/07/21 → 22/07/21

Bibliographical note

Publisher Copyright:
© 2021, Springer Nature Switzerland AG.

Access to Document

10.1007/978-3-030-79121-6_15

Cite this

Arbitman, G., Klein, S. T., Peterlongo, P., & Shapira, D. (2021). Approximate Hashing for Bioinformatics. In S. Maneth (Ed.), Implementation and Application of Automata - 25th International Conference, CIAA 2021, Proceedings (pp. 178-189). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12803 LNCS). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-030-79121-6_15

Arbitman, Guy ; Klein, Shmuel T. ; Peterlongo, Pierre et al. / Approximate Hashing for Bioinformatics. Implementation and Application of Automata - 25th International Conference, CIAA 2021, Proceedings. editor / Sebastian Maneth. Springer Science and Business Media Deutschland GmbH, 2021. pp. 178-189 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Arbitman, G, Klein, ST, Peterlongo, P & Shapira, D 2021, Approximate Hashing for Bioinformatics. in S Maneth (ed.), Implementation and Application of Automata - 25th International Conference, CIAA 2021, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12803 LNCS, Springer Science and Business Media Deutschland GmbH, pp. 178-189, 25th International Conference on Implementation and Application of Automata, CIAA 2021, Virtual, Online, 19/07/21. https://doi.org/10.1007/978-3-030-79121-6_15

Approximate Hashing for Bioinformatics. / Arbitman, Guy; Klein, Shmuel T.; Peterlongo, Pierre et al.
Implementation and Application of Automata - 25th International Conference, CIAA 2021, Proceedings. ed. / Sebastian Maneth. Springer Science and Business Media Deutschland GmbH, 2021. p. 178-189 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12803 LNCS).

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

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Arbitman G, Klein ST, Peterlongo P, Shapira D. Approximate Hashing for Bioinformatics. In Maneth S, editor, Implementation and Application of Automata - 25th International Conference, CIAA 2021, Proceedings. Springer Science and Business Media Deutschland GmbH. 2021. p. 178-189. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-030-79121-6_15

Approximate Hashing for Bioinformatics

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