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.
|Effektiv start/slut dato||01/09/2013 → 30/09/2016|