a chinese postman problem based on dna computing z. yin, f. zhang, and j. xu* j. chem. inf. comput....

A Chinese Postman Problem A Chinese Postman Problem Based on DNA ComputingBased on DNA Computing

Z. Yin, F. Zhang, and J. Xu*J. Chem. Inf. Comput. Sci. 2002, 42, 2

22-224

Summarized by Shin, Soo-Yong2002. 10. 11

© 2002, SNU BioIntelligence Lab, http://bi.snu.ac.kr/

Chinese Postman Problem Chinese Postman Problem (CPP)(CPP) Similar with TSP CPP has to visit all edges in the graph, but ca

n visit same edges more than twice. cf) TSP for all vertexes.


Algorithm for CPPAlgorithm for CPP

The same as Adleman’s algorithm

1. Generate a random closed walk2. Keep only those closed walks that begins with fixed v

ertices and end with fixed vertices3. Keep only those closed walks that enter all of the ed

ges of the given graph at least once.4. Find the shortest path5. Determine


ImplementationImplementation

Step 1 Edge weights are represented by the length. Vertex : 20mer Edge : 10mer for starting, 10mer for ending, 10*wij

for weight


ImplementationImplementation

Step 2 PCR with rear 10 bp of ‘0’ and former 10 bp of ‘0’

Step 3 Affinity-purification for all edges

Step 4 Gel electrophoresis

Step 5 Sequencing


참고사항참고사항

실험 없음 . Journal of Chemical Information and Computer

Science Core SCI! impact factor is 1.777 (1998)

DNA Solution of a DNA Solution of a Graph Coloring ProblemGraph Coloring Problem

Y. Liu, J. Xu*, L. Pan, and S. WangJ. Chem. Inf. Comput. Sci. 2002, 42, 5

24-528

Summarized by Shin, Soo-Yong


Graph Coloring ProblemGraph Coloring Problem

Find minimum number of color to paint a different color for the adjacent vertexes.


AlgorithmAlgorithm

Convert to the problem an ensemble of all rearrangements of the required colors. Ex) (2,1,5,3,6,5) (1,2,3,1,2,3) (2,3,4,2,3,4) Wrong answer : (1,1,3,1,2,3)

Delete illegal answer Sort the answer (find minimum length)


RepresentationRepresentation

dsDNA strands Color section (Ci) and name section (Ni)

N1 & N7 for PCR, Ni : 20 bp Ci : 10 + 5j if Ci = j (j = 1,2,…,6) 380 bp for 666666, 230 bp for 111111


Representation Representation

Initial fragment


Making a poolMaking a pool

Parallel overlap assembly (POA)


Delete illegal answerDelete illegal answer

Illegal answer template (x, x, *, *, *, *), (x, *, x, *, *, *), (x, *, *, *, x, *),

(x, *, *, *, *, x), (*, x, x, *, *, *), (*, x, *, x, *, *), (*, x, *, *, *, x), (*, *, x, x, *, *), (*, *, x, *, x, *), (*, *, *, x, x, *), (*, *, *, x, *, x), (*, *, *, *, x, x)

Divide into two tubes T1 cut out by restriction enzyme (1, *, *, *, *,

*) T2 cut out (*, 1, *, *, *, *)

Combine T1 and T2 Repeat all strings for given templates.


Experimental ResultsExperimental Results

Product of POA and PCR

Final product


To reduce errorsTo reduce errors

Digesting the ssDNA with S1 nuclease before restriction digestions

Two cycles of digestion-PCR Avoid accidental homologies longer than 4 bp

a chinese postman problem based on dna computing z. yin, f. zhang, and j. xu* j. chem. inf. comput....

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