Compact universal k-mer hitting sets

Yaron Orenstein; David Pellow; Guillaume Marçais; Ron Shamir; Carl Kingsford

doi:10.1007/978-3-319-43681-4_21

Compact universal k-mer hitting sets

Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford

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

24 Scopus citations

Abstract

We address the problem of finding a minimum-size set of k-mers that hits L-long sequences. The problem arises in the design of compact hash functions and other data structures for efficient handling of large sequencing datasets. We prove that the problem of hitting a given set of L-long sequences is NP-hard and give a heuristic solution that finds a compact universal k-mer set that hits any set of L-long sequences. The algorithm, called DOCKS (design of compact k-mer sets), works in two phases: (i) finding a minimum-size k-mer set that hits every infinite sequence; (ii) greedily adding k-mers such that together they hit all remaining L-long sequences. We show that DOCKS works well in practice and produces a set of k-mers that is much smaller than a random choice of k-mers. We present results for various values of k and sequence lengths L and by applying them to two bacterial genomes show that universal hitting k-mers improve on minimizers. The software and exemplary sets are freely available at acgt.cs.tau.ac.il/docks/.

Original language	English
Title of host publication	Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings
Editors	Martin Frith, Christian Nørgaard Storm Pedersen
Publisher	Springer Verlag
Pages	257-268
Number of pages	12
ISBN (Print)	9783319436807
DOIs	https://doi.org/10.1007/978-3-319-43681-4_21
State	Published - 2016
Externally published	Yes
Event	16th International Workshop on Algorithms in Bioinformatics, WABI 2016 - Aarhus, Denmark Duration: 22 Aug 2016 → 24 Aug 2016

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9838 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	16th International Workshop on Algorithms in Bioinformatics, WABI 2016
Country/Territory	Denmark
City	Aarhus
Period	22/08/16 → 24/08/16

Bibliographical note

Publisher Copyright:
© Springer International Publishing Switzerland 2016.

Funding

R.S. was supported in part by the Israel Science Foundation as part of the ISF-NSFC joint program 2015–2018. D.P. was supported in part by a Ph.D. fellowship from the Edmond J. Safra Center for Bioinformatics at Tel-Aviv University. This research is funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4554 to C.K., by the US National Science Foundation (CCF-1256087, CCF-1319998) and by the US National Institutes of Health (R01HG007104). C.K. received support as an Alfred P. Sloan Research Fellow. Part of this work was done while Y.O., R.S. and C.K. were visiting the Simons Institute for the Theory of Computing.

Funders	Funder number
ISF-NSFC
National Science Foundation	CCF-1256087, CCF-1319998, 1319998
National Institutes of Health	R01HG007104
Gordon and Betty Moore Foundation	GBMF4554
Israel Science Foundation

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10.1007/978-3-319-43681-4_21

Cite this

Orenstein, Y., Pellow, D., Marçais, G., Shamir, R., & Kingsford, C. (2016). Compact universal k-mer hitting sets. In M. Frith, & C. N. S. Pedersen (Eds.), Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings (pp. 257-268). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9838 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-43681-4_21

Orenstein, Yaron ; Pellow, David ; Marçais, Guillaume et al. / Compact universal k-mer hitting sets. Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. editor / Martin Frith ; Christian Nørgaard Storm Pedersen. Springer Verlag, 2016. pp. 257-268 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "We address the problem of finding a minimum-size set of k-mers that hits L-long sequences. The problem arises in the design of compact hash functions and other data structures for efficient handling of large sequencing datasets. We prove that the problem of hitting a given set of L-long sequences is NP-hard and give a heuristic solution that finds a compact universal k-mer set that hits any set of L-long sequences. The algorithm, called DOCKS (design of compact k-mer sets), works in two phases: (i) finding a minimum-size k-mer set that hits every infinite sequence; (ii) greedily adding k-mers such that together they hit all remaining L-long sequences. We show that DOCKS works well in practice and produces a set of k-mers that is much smaller than a random choice of k-mers. We present results for various values of k and sequence lengths L and by applying them to two bacterial genomes show that universal hitting k-mers improve on minimizers. The software and exemplary sets are freely available at acgt.cs.tau.ac.il/docks/.",

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Orenstein, Y, Pellow, D, Marçais, G, Shamir, R & Kingsford, C 2016, Compact universal k-mer hitting sets. in M Frith & CNS Pedersen (eds), Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9838 LNCS, Springer Verlag, pp. 257-268, 16th International Workshop on Algorithms in Bioinformatics, WABI 2016, Aarhus, Denmark, 22/08/16. https://doi.org/10.1007/978-3-319-43681-4_21

Compact universal k-mer hitting sets. / Orenstein, Yaron; Pellow, David; Marçais, Guillaume et al.
Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. ed. / Martin Frith; Christian Nørgaard Storm Pedersen. Springer Verlag, 2016. p. 257-268 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9838 LNCS).

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

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Orenstein Y, Pellow D, Marçais G, Shamir R, Kingsford C. Compact universal k-mer hitting sets. In Frith M, Pedersen CNS, editors, Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Springer Verlag. 2016. p. 257-268. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-43681-4_21

Compact universal k-mer hitting sets

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