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SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

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Bioinformatics Research and Applications (ISBRA 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6674))

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Abstract

The recent interest in function of various RNA structures, reflected in the growth of solved RNA structures in PDB, calls for methods for effective and efficient similarity search in RNA structural databases. Here, we propose a method called SETTER (RNA SEcondary sTructure-based TERtiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (GSSU). We introduce a fast similarity method exploiting RMSD-based algorithm allowing to assess distance to a pair of GSSU, and a method for aggregating these partial distances into a final distance corresponding to structural similarity of the examined RNA structures. Our algorithm yields not only the distance but also a superposition allowing to visualize the structural similarity. Comparative experiments show that our proposed method is competitive with the best existing solutions, both in terms of effectiveness and efficiency.

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Author information

Authors and Affiliations

  1. FMP, Department of Software Engineering, Charles University in Prague, Malostranské nám. 25, 118 00, Prague, Czech Republic

    David Hoksza

  2. Laboratory of Informatics and Chemistry, Institute of Chemical Technology Prague, Technická 5, 166 28, Prague, Czech Republic

    Daniel Svozil

Authors
  1. David Hoksza
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  2. Daniel Svozil
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, Texas A&M University, 77843-3112, College Station, TX, USA

    Jianer Chen

  2. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

  3. Department of Computer Science, Georgia State University, 30303, Atlanta, GA, USA

    Alexander Zelikovsky

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Hoksza, D., Svozil, D. (2011). SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm. In: Chen, J., Wang, J., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science(), vol 6674. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21260-4_8

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  • DOI: https://doi.org/10.1007/978-3-642-21260-4_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21259-8

  • Online ISBN: 978-3-642-21260-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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