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Python code for PCR simulation

This project involves computer simulation of PCR (Polymerase Chain Reaction). It is to be done in your project group. The effort and responsibilities of the students in a group must be clearly enough delimited and stated in a statement (attached to your project report) so that each of you can be graded fairly and separately.

Introduction

As you’ve figured out, the purpose of PCR ([login to view URL]) is to make huge number of copies of a DNA segment. There are three major steps in PCR: denaturizing, annealing and elongation. Here is a figure that illustrates the process ([login to view URL]~avierstr/principles/[login to view URL]). Hope it will be helpful for some of our computer science students. On this web site you can also find a computer animation of PCR process ([login to view URL]~avierstr/principles/[login to view URL]).

PCR steps

In this project you will write a computer program to simulate the PCR process.

Program Specifications:

Your computer program should be written in Python. If any one of you would like to use any other language, he/she needs to get the approval of the entire group.

Inputs:

1. You may assume you have favorable experimental conditions throughout your simulation.

2. Your original DNA template is of n base-pairs (assume n = 2000 for your test case if you generate your template randomly).

3. The size of the DNA segment to be amplified is m (assume m = 200 if the template is generated randomly).

4. You may also assume that the length of the original forward and backward primers are fixed at p bases (assume p = 20).

5. The processivity of the taq polymerase (“fall-off rate”) is d+r, where d is a fixed constant, and r is a random number between [-e, e], (assume d = 200, e=50).

Note: The numbers stated above are rough estimates, not corresponding to the true numbers in any living organism. Use your choices if they make more sense to you. You may simulate only 10 PCR cycles if your computation power is limited. The initial template can be generated randomly. Primers are designed based on this template.

Your output: (What you might see on the gel)

1. Statistics of the PCR products:

(a) Number of DNA fragments;

(b) Average length of DNA fragments;

(c) Distribution of the lengths of the DNA fragments (you may use column chart to show your result).

2. Other things you find interesting.

Skills: Python

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