1. Simulation of Hybridization
Jang HaYoung

2. NACST/Sim Lab experiment simulation tool
Hybridization, PCR, gel electrophoresis
Using thermodynamic data & artificial chemistry
Hybridization simulator
© 2003 SNU CSE Biointelligence Lab

3. © 2003 SNU CSE Biointelligence Lab
NACST/Sim
Virtual Hybridization
Essential to almost all the lab experiment.
First step to simulation of lab experiment.
© 2003 SNU CSE Biointelligence Lab

4. © 2003 SNU CSE Biointelligence Lab
NACST/Sim
Nearest Neighbor method with 1-base mismatch
© 2003 SNU CSE Biointelligence Lab

5. © 2003 SNU CSE Biointelligence Lab
NACST/Sim
Nearest Neighbor method
CGTACCTTAGGCT
AGCTTAGGATGGCATGGAATCCGATGCATGGC
© 2003 SNU CSE Biointelligence Lab

6. © 2003 SNU CSE Biointelligence Lab
NACST/Sim
Difficulties
© 2003 SNU CSE Biointelligence Lab

7. © 2003 SNU CSE Biointelligence Lab
NACST/Sim
Difficulties
Nearest Neighbor method?
How can handle chain reaction?
What is the reasonable size of the tube?
How can detect the result?
© 2003 SNU CSE Biointelligence Lab

8. © 2003 SNU CSE Biointelligence Lab
NACST/Sim
Objective
Parallelize?
Refine the data structure
Use sigmoid function as decision maker
Handle the bulge and hairpin
© 2003 SNU CSE Biointelligence Lab

9. DNA/RNA Secondary Structure
Thermodynamic method: Free Energy minimization– Zuker algorithm.
Phylogenetic comparative method
Grammar induction method
Molecular Dynamics
© 2003 SNU CSE Biointelligence Lab

10. DNA/RNA Secondary Structure
Grammar induction method
Use stochastic context-free grammar
Parse tree of the sequences represents the secondary sturcture
A kind of thermodynamic method
How can design the grammar?
© 2003 SNU CSE Biointelligence Lab