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Exact Search Algorithms for Biological Sequences

Eric Rivals 1, * Leena Salmela 2, 3 Jorma Tarhio 2, 3
* Corresponding author
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Pattern matching is a fundamental task in text analyzes, and hence have been heavily exploited in bioinformatics where DNA, RNA, and amino-acid macromolecules are represented as sequences over an alphabet of residue. Examples of analyzes include regulatory motif search and inference, gene identification, repeat finding, association discovery in biomedical literature, etc. We provide an overview of techniques for efficient search of a single or multiple patterns in sequences.
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Submitted on : Thursday, September 8, 2011 - 2:21:42 PM
Last modification on : Monday, January 13, 2020 - 5:36:13 PM
Long-term archiving on: : Friday, December 9, 2011 - 2:22:52 AM


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  • HAL Id : lirmm-00620723, version 1



Eric Rivals, Leena Salmela, Jorma Tarhio. Exact Search Algorithms for Biological Sequences. Mourad Elloumi and Albert Y. Zomaya. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, John Wiley & Sons, Inc., pp.91-111, 2011, Wiley Series in Bioinformatics, 978-0-470-50519-9. ⟨lirmm-00620723⟩



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