PT45: Hamid Reza Chitsaz - A Partition Function... - ISMB/ECCB Stockholm 2009

First part presented by Raheleh Salari - Roland Krause

Increased interest in RNA-RNA interaction prediction requires computational target prediction. - Roland Krause

ncRNAs bind to mRNA and regulate translation, including the specificity etc. - Roland Krause

Several models have been described, e.g. PairFold, RNAhybrid, RNAup, IRIS, InteRNA. - Roland Krause

Problem np-complete - Roland Krause

All current approaches do not include the probability and stability of the joint secondary structure. - Roland Krause

Interaction energy model and interaction partition function over all SS without pseudoknots or crossing interactions and zigzags. - Roland Krause

The standard model by Matthews et al (1999) assumes an energy model with independence between hairpins, bulges etc. - Roland Krause

More than one loop-loop interaction in a real example, ignore interhybrid loop, other loops termed kissing loops. - Roland Krause

# that was a little fast - Roland Krause

A kissing loop is intramolecular loop that makes interaction with the other strand. - Roland Krause

Give the energy functions for the new structures for the interaction partition function. - Roland Krause

Second part given now by Hamid Chitsaz - Roland Krause

Main interest in the strength and stability of the RNA interaction, which is challenging because all structures must be accounted for exactly once. - Roland Krause

Make use of a dynamic programming approach using divide and conquer. Compute the partition function for bits of the structure. - Roland Krause

McCaskill's algorithm (1990) is introduced, describing a participation function for single strands. - Roland Krause

For two unpaired strands, McCaskill's algorithm can be used directly, - Roland Krause

98 cases need to be considered, not even in the paper but in the suppl. mat. - Roland Krause

# sounds like a complicated model, it's not completely presented - Roland Krause

Explanation for the no-zig zag assumption motivated by less running time, one arch describes them all. - Roland Krause

Can predict the equilibrium concentaion, the melting temperature and the UV absorption. - Roland Krause

Presented algorithm (piRNA) outperforms existing ones by an order of magnitude, experimental validation with Tm shows little deviation. - Roland Krause

Algorithm is available. - Roland Krause