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Adelman's DNA Algorithm For Hamiltonian Path: Step 1

The document provides examples and explanations of Hamiltonian path method for DNA computing and phylogenetic trees. It describes Adelman's algorithm for finding a Hamiltonian path using DNA strands to represent paths in a graph from a start to end node. It also explains how gel electrophoresis and PCR can be used to remove invalid paths. Two types of phylogenetic trees are defined - a perfect phylogenetic tree where each gene change can only occur once, and an ultrametric tree where the distance from any internal node to its leaves is constant. An example perfect phylogeny is given using a character state matrix to construct a tree.

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temper bhanu
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95 views

Adelman's DNA Algorithm For Hamiltonian Path: Step 1

The document provides examples and explanations of Hamiltonian path method for DNA computing and phylogenetic trees. It describes Adelman's algorithm for finding a Hamiltonian path using DNA strands to represent paths in a graph from a start to end node. It also explains how gel electrophoresis and PCR can be used to remove invalid paths. Two types of phylogenetic trees are defined - a perfect phylogenetic tree where each gene change can only occur once, and an ultrametric tree where the distance from any internal node to its leaves is constant. An example perfect phylogeny is given using a character state matrix to construct a tree.

Uploaded by

temper bhanu
Copyright
© © All Rights Reserved
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Download as DOCX, PDF, TXT or read online on Scribd
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Digital Assignment -2

Name:BHANU
PRAKASH N

Regno.:17mis1063

1. Explain Hamiltonian path method in details for DNA computing with suitable examples

Adelman’s DNA algorithm for Hamiltonian Path:


Input: A directed graph with A directed graph with n nodes including a nodes
including a start node A and an end node B. end node B.
Step 1: Generate random paths through the graphs of the Generate random
paths through the graphs of the above form, randomly, and in large quantities .
above form, randomly, and in large quantities.
Step 2: Remove all paths that do not begin with Remove all paths that do not
begin with start node A start node A and end with end node B. and end with
end node B.
Step 3: If the graph has If the graph has n nodes, then keep only those nodes,
then keep only those paths that enter exactly paths that enter exactly n nodes.
Step 4: Remove any paths that repeat nodes. This is done Remove any paths
that repeat nodes. This is done by filtering out filtering out all paths that have
no node V all paths that have no node Vi, for all V, for all.
step 5. If any path remains then answer “yes” otherwise “no”.

DNA Computing for the problem given problem :


Step 1 : To each node “i” of the graph is associated a random
20 base string 20 base string (of the 4 bases A,G,C,T).
For each directed (arrowed) edge (node “i” to node “j”) of
the graph, associate a 20 base DNA string, called “S-i-j”
whose –
a) left half is the DNA complement (i.e. c) of the right half of
S-i,
b) right half is the DNA complement of the left half of S-j.
Step 2: Use PCR to remove bad starts and remove bad starts
and ends.
Selectively Selectively amplify amplify DNA strands that DNA
strands that represent represent paths from correct starting
city from correct starting city (node) A to destination city B
(node) A to destination city B (use Polymerase Polymerase
Chain Reaction—PCR Chain Reaction—PCR). Number of
other paths is negligible.
Step 2a. Step 2a. Denature Denature and add node add node
0 primer 0 primer and node 6 anti-primer and node 6 anti-
primer
Step2b: Step2b: PCR amplifies 0-6 strands PCR amplifies 0-6
strands

Step 3: Step 3: Use Gel Electrophoresis to remove Use Gel


Electrophoresis to remove too long (and too short) paths too
long (and too short) paths.

Step 4: Affinity Purification.


Step5: PCR amplify remaining product.
Hamiltonian path as an example of path as an example of
graph theory problem

The Hamiltonian path problem , In a directed graph, find a


path from one node that visits find a path from one node
that visits (following allowed routes) each node (following
allowed routes) each node exactly once.

2. Explain in details with example 1. Ultrametric tree 2.


Perfect phylogenetic tree
Perfect phylogeny :
Each change can happen only once and is not reversible.
Example: Consider binary characters. Each character
corresponds to a gene. 0-gene absent 1-gene present It make
sense to assume directed changes only form 0 to 1.
The root has to be all zeros Perfect phylogeny Example:
characters = genes; 0 = absent ; 1 = present Taxa: genomes
(A,B,C,D,E) A 0 0 0 1 1 0 B 1 1 0 0 0 0 C 0 0 0 1 1 1 D 1 0 1 0 0
0 E 0 0 0 1 0 0 genes B D E A C
Perfect phylogeny tree Goal: For a given character state
matrix construct a tree topology that provides perfect
phylogeny.

Ultrametric trees:
• The distance from any internal node C to any of its leaves is
constant and equal to h(C)
• For each node (v) we keep variable h – height of the node
in the tree. h(v) = 0 for all leaves.

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