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Using Carrillo-Lipman Approach to Speed up Simultaneous Alignment and Folding of RNA Sequences

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Adaptive and Natural Computing Algorithms (ICANNGA 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7824))

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Abstract

Multiple sequence alignment and RNA folding are two important tasks in the field of bioinformatics. Solving those problems simultaneously leads to biologically more significant results. The only one currently known precise algorithm (Sankoff) is too much computationaly expensive for such long sequences. In this work we introduce a new algorithm, that is a combination of well known Nussinov folding algorithm and Sankoff quadratic alignment algorithm and a speed-up for this algorithm that is inspired by the Carrillo-Lipman algorithm for the multiple sequence alignment problem. This approach may allow us to simultaneously align and fold more than two sequences in a better time than we can do it using the Sankoff algorithm.

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Author information

Authors and Affiliations

  1. Institute of Computer Science, Pavol Jozef Šafárik University in Košice, Jesenná 5, Košice, Slovak Republic

    Mária Šimaľová

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  1. Mária Šimaľová
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Editors and Affiliations

  1. Départment des Systémes d’Information, Quartier UNIL-Dorigny, Bâtiment Internef, Université de Lausanne, 105, Lausanne, Switzerland

    Marco Tomassini , Alberto Antonioni , Fabio Daolio  & Pierre Buesser , ,  & 

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Šimaľová, M. (2013). Using Carrillo-Lipman Approach to Speed up Simultaneous Alignment and Folding of RNA Sequences. In: Tomassini, M., Antonioni, A., Daolio, F., Buesser, P. (eds) Adaptive and Natural Computing Algorithms. ICANNGA 2013. Lecture Notes in Computer Science, vol 7824. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37213-1_34

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  • DOI: https://doi.org/10.1007/978-3-642-37213-1_34

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-37212-4

  • Online ISBN: 978-3-642-37213-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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