Automated rendering of multi-stranded DNA complexes with pseudoknots

TL;DR

This paper introduces a fast, general method for converting textual descriptions of multi-stranded DNA complexes, including pseudoknotted structures, into clear 2D diagrams, with efficient algorithms for both planar and non-planar cases.

Contribution

The paper presents a novel algorithm that efficiently renders complex DNA structures with pseudoknots into 2D diagrams, handling both planar and non-planar cases.

Findings

Linear-time planar rendering when possible

Quadratic-time approximate rendering for non-planar structures

Examples demonstrating the method's effectiveness

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.