Automated rendering of multi-stranded DNA complexes with pseudoknots

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.Comment: 12 pages, 7 figure

Minimum depth graph embedding

Abstract. The depth of a planar embedding is a measure of the topological nesting of the biconnected components of the graph. Minimizing the depth of planar embeddings has important practical applications to graph drawing. We give a linear time algorithm for computing a minimum depth embedding of a planar graphs whose biconnected components have a prescribed embedding.