Seminar 1 : RNA Sequence Design

Speaker: Vladimir Reinharz
Title: RNA Sequence Design

Abstract:
RNAs are biomolecules that can be seen as words in {ACGU}+. An interesting mathematical representation of the structure as a dot bracket sequence [e.g. (((…))) ] has been shown to have some ressemblance with reality. Having an energy model derived from experiments, the ensemble of structures given a sequence has been completely characterized in the 70s (in this model). At the opposite, given a structure, knowing if it exists a sequence with an affinity higher than some threshold  is believed to be NP-hard. I developed an algorithm based on the inside-outside to, given a structure, do a global stochastic Boltzmann sampling of sequences in linear time. I will also talk of a few potential applications in drug design and bioengineering. It has been implemented in a tool called incaRNAtion

http://dx.doi.org/10.1093/bioinformatics/btt217