predict the secondary structure Given a primary structure of an RNA, ﬁnd a secondary structure that maximizes the number of base pairs Tuesday, April 24, 12

sequences which are structurally similar (Sankoff, Gary and Stormo) Structure prediction based on a single RNA sequence Nussinov Folding Algorithm, Zuker Algorithm Tuesday, April 24, 12

The hydrogen bond at a base pair tries to stabilize the structure Free bases inside a loop tries to disrupt the structure Difference between these two is the destabilizing energy Given a primary structure of an RNA, ﬁnd the secondary structure with least total energy Tuesday, April 24, 12

structure eS(i, j) is negative Hairpin : eH(i, j) The bigger the loop, the more unstable the structure is eH(i, j) depends on |j-i+1| Tuesday, April 24, 12

i', j') The bigger the loop is and the more asymmetric the two sides are, the more unstable is the structure eL(i, j, i', j') depends on (|i'-i+1|+|j'-j+1|) and the asymmetry Multi-loop : eM(i1, j1, i2, j2, ..., ik, jk) The structure is more unstable if the loop size and k is big Tuesday, April 24, 12

the maximum number of base pairs Future works Develop an algorithm that does not make the assumption of absence of pseudoknots (Gary and Stormo) Develop an algorithm that addresses base triples and other types of base pairs Tuesday, April 24, 12