Villum Fonden - Teknisk og naturvidenskabelig forskning - Postdoc-programme - 24 mdr's postdoc stipendie - A new folding algorithm for RNA pseudoknot structures

  • Reidys, Christian (Head coordinator)

Project: Research

Project Details


In this proposal we devise a new folding algorithm for RNA pseudoknot structures. This new fold is obtained by considering a topological filtration of RNA structures and specific build principles observed in these. Our proposal breaks the current folding paradigm replacing recursions based on sequence length by recursions based on topological genus. These new recursions are formulated over fatgraphs a slightly enriched version of simple graphs. Fatgraphs correspond to topological surfaces and are therefore filtered by topological genus. In this new language the genus reduction is very intuitive and can be visualized by “slicing” vertices. The proposal is motivated by recent discoveries in the context of topological RNA structures, in particular the observation that topological boundary components and loops, central for energy calculations in these molecules are identical. This proposal will significantly advance the mathematics and folding of RNA pseudoknot and RNA-RNA interaction structures.
Effective start/end date01/09/201330/09/2016