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Identification de motifs au sein des structures biologiques arborescentes

Abstract : The explosion of available biological data urges the need for bioinformatics methods. Many biological structures are modeled by tree structures such as RNA secondary structure and plants architecture. These structures contain repeating units within their structure, but also between different structures. We propose to exploit this fundamental property to improve storage and treatment of such objects. Following the principle of sequence filtering, we define a filtering method on ordered trees to efficiently retrieve in a database a set of ordered trees close from a query. The method is based on a decomposition of the tree into seeds and the detection of shared seeds between these structures. We define and solve the maximum chaining problem on trees. We propose for RNA secondary structure applications a definition of (l−d) centered seed. Based on instantiation techniques used for instance in computer graphics and the repetitiveness of biological structures, we present a compression method which reduces the memory space required for plant architecture storage. A more compact data structure is used in order to represent plant architecture. The construction of this data structure require the identification of internal redundancies and taking into account both topological and geometrical informations.
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Contributor : Anne-Laure Gaillard <>
Submitted on : Thursday, December 15, 2011 - 10:20:14 AM
Last modification on : Thursday, January 11, 2018 - 6:20:16 AM
Long-term archiving on: : Monday, December 5, 2016 - 3:33:32 AM


  • HAL Id : tel-00652227, version 1


Anne-Laure Gaillard. Identification de motifs au sein des structures biologiques arborescentes. Bio-informatique [q-bio.QM]. Université Sciences et Technologies - Bordeaux I, 2011. Français. ⟨tel-00652227⟩



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