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Subset Seed Automaton

descriptionPublicationkeyboard_double_arrow_right Part of book or chapter of book , Article , Preprint , Other literature type , Conference object 27 Oct 2007Embargo end date: 01 Jan 2014 France English Publisher:Springer Berlin Heidelberg

Authors: Kucherov, Gregory; Noé, Laurent; Roytberg, Mihkail;

doi: 10.1007/978-3-540-76336-9_18 , 10.48550/arxiv.1408.6198

arXiv: http://arxiv.org/abs/1408.6198

Subset Seed Automaton

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Abstract

We study the pattern matching automaton introduced in (A unifying framework for seed sensitivity and its application to subset seeds) for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much smaller than the one obtained by applying the Aho-Corasick construction. We study properties of this automaton and present an efficient implementation of the automaton construction. We also present some experimental results and show that this automaton can be successfully applied to more general situations.

12 pages, 2 figures, 2 tables, CIAA 2007, http://hal.inria.fr/inria-00170414/en/

Country

France

Related Organizations

French National Centre for Scientific Research
France
French Institute for Research in Computer Science and Automation
France
Institute of Mathematical Problems of Biology
Russian Federation
French Institute for Research in Computer Science and Automation
France

Keywords

FOS: Computer and information sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Formal Languages and Automata Theory (cs.FL), F.1.1; F.4.3, [INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS], Computer Science - Formal Languages and Automata Theory, 20M35, 68Q45, Quantitative Biology - Quantitative Methods, [INFO.INFO-CL] Computer Science [cs]/Computation and Language [cs.CL], FOS: Biological sciences, Computer Science - Data Structures and Algorithms, F.4.3, Data Structures and Algorithms (cs.DS), F.1.1, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

3 Research products, page of 1

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