RNA Secondary Structure
™ RNA is a sequence of nucleotides
ƒ Adenine, Guanine, Cytosine, Uracil
™ Adenine pairs with Uracil, and
Cytosine pairs with Guanine by a
hydrogen bond
™ The paring makes the RNA
sequence fold upon itself, resulting
a secondary structure of RNA
RNA Secondary Structure
™ RNA is a sequence of
nucleotides
ƒ Adenine, Guanine, Cytosine,
AUracil
C U C C G A G U
™ Adenine pairs with Guanine,
and Cytosine pairs with
Uracil by a hydrogen bond
™ The paring make the RNA
sequence
. upon
) )
. ) itself,
( ( ( .fold
resulting the secondary
structure of RNA
Various Substructures
Secondary Structure and Energy
™ Two pairs of nucleotides reduce the total free energy
of RNA molecule by stacking on each other
™ Loops increase the total free energy of RNA molecule
+4.1
-1.7
-2.1
™ Biologists wants to predict the secondary structure
with minimum free energy
HW3. RNA Secondary Structure Prediction
™ Write a Prolog program that
ƒ given a sequence of RNA,
ƒ predicts the secondary structure with minimum free energy
™ The program should print
ƒ The predicted structure
• with ‘(‘, ‘.’, and ‘)’
ƒ Free energy of the structure
™ Efficiency and correctness will be the measure
™ Detailed energy data will be distributed
™ Until 4/26 3:30pm