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Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots

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Unconventional Computation and Natural Computation (UCNC 2024)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 14776))

Abstract

We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted, and if a planar rendering is possible, the method will determine one in time which is essentially linear in the size of the textual description. (That is, except for a final stochastic fine-tuning step.) If a planar rendering is not possible, the method will compute a visually pleasing approximate rendering in quadratic time. Examples of diagrams produced by the method are presented in the paper.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Aalto University, Espoo, Finland

    Małgorzata Nowicka & Pekka Orponen

  2. Department of Chemical Engineering, NTNU, Trondheim, Norway

    Vinay K. Gautam

Authors
  1. Małgorzata Nowicka
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  2. Vinay K. Gautam
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  3. Pekka Orponen
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Correspondence to Pekka Orponen .

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Editors and Affiliations

  1. Ajou University, Suwon, Korea (Republic of)

    Da-Jung Cho

  2. Pohang University of Science and Technology, Pohang, Korea (Republic of)

    Jongmin Kim

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Nowicka, M., Gautam, V.K., Orponen, P. (2024). Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots. In: Cho, DJ., Kim, J. (eds) Unconventional Computation and Natural Computation. UCNC 2024. Lecture Notes in Computer Science, vol 14776. Springer, Cham. https://doi.org/10.1007/978-3-031-63742-1_14

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  • DOI: https://doi.org/10.1007/978-3-031-63742-1_14

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