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An Edit Distance Between RNA Stem-Loops

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String Processing and Information Retrieval (SPIRE 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3772))

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Abstract

We introduce the notion of conservative edit distance and mapping between two RNA stem-loops. We show that unlike the general edit distance between RNA secondary structures, the conservative edit distance can be computed in polynomial time and space, and we describe an algorithm for this problem. We show how this algorithm can be used in the more general problem of complete RNA secondary structures comparison.

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References

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Author information

Authors and Affiliations

  1. Programme de Bioinformatique, Université de Montréal, Pav. André-Aisenstadt, CP 6128 succ. Centre-ville, Montréal, (QC), H3C 3J7, Canada

    Valentin Guignon

  2. LaCIM, Département d’Informatique, Université du Québec à Montréal, C.P. 8888 succ. Centre-Ville, Montréal, (QC), H3C 3P8, Canada

    Cedric Chauve

  3. LBIT, DIRO, Université de Montréal, Pav. André-Aisenstadt, CP 6128 succ. Centre-ville, Montréal, (QC), H3C 3J7, Canada

    Sylvie Hamel

Authors
  1. Valentin Guignon
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  2. Cedric Chauve
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  3. Sylvie Hamel
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Editor information

Editors and Affiliations

  1. University of Toronto,  

    Mariano Consens

  2. Dept. of Computer Science, University of Chile,  

    Gonzalo Navarro

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© 2005 Springer-Verlag Berlin Heidelberg

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Guignon, V., Chauve, C., Hamel, S. (2005). An Edit Distance Between RNA Stem-Loops. In: Consens, M., Navarro, G. (eds) String Processing and Information Retrieval. SPIRE 2005. Lecture Notes in Computer Science, vol 3772. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11575832_38

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  • DOI: https://doi.org/10.1007/11575832_38

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29740-6

  • Online ISBN: 978-3-540-32241-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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