Automated rendering of multi-stranded DNA complexes with pseudoknots

Malgorzata Nowicka, Vinay K Gautam, Pekka Orponen*

*Corresponding author for this work

Research output: Other contributionScientific

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.
Original languageEnglish
PublisherarXiv.org
Number of pages12
DOIs
Publication statusPublished - 11 Aug 2023
MoE publication typeNot Eligible

Keywords

  • DNA strand displacement
  • DSD systems
  • multi-strand DNA
  • pseudoknots
  • graph drawing
  • visualisation

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