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Module3 Bioinformatics Algorithms

This document provides an introduction to a module on bioinformatics algorithms. It discusses basic algorithms, Python programming, and practical sessions. It introduces problems related to DNA replication, finding origins of replication, and frequent word problems. It provides an overview of Python, how to set up a Python environment, and tutorials for learning Python basics. It also introduces the Rosalind bioinformatics problem solving platform and recommends starting with the Python Village or Bioinformatics Stronghold tracks.

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nguyenquynhnhungt65
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36 views16 pages

Module3 Bioinformatics Algorithms

This document provides an introduction to a module on bioinformatics algorithms. It discusses basic algorithms, Python programming, and practical sessions. It introduces problems related to DNA replication, finding origins of replication, and frequent word problems. It provides an overview of Python, how to set up a Python environment, and tutorials for learning Python basics. It also introduces the Rosalind bioinformatics problem solving platform and recommends starting with the Python Village or Bioinformatics Stronghold tracks.

Uploaded by

nguyenquynhnhungt65
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© © All Rights Reserved
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Download as pdf or txt
Download as pdf or txt
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July, 2021

INTRODUCTION TO BIOINFORMATICS

Instructor: Dang Thi Minh Nguyet


French National Research Institue for Sustainable Development (IRD) – University of Montpellier
MODULE 3: INTRODUCTION TO BIOINFORMATICS
ALGORITHMS

• Basic algorithms

• Python Programming

• Practical sessions
MODULE 3: INTRODUCTION TO BIOINFORMATICS
ALGORITHMS

• Basic algorithms

• Python Programming

• Practical sessions
DNA REPLICATION PROBLEMS
FINDING ORIGIN OF REPLICATION PROBLEMS

Does this problem represent a clearly stated computational problem?


HIDDEN MESSAGES IN THE REPLICATION ORIGIN

Does this problem represent a clearly stated computational problem?


FREQUENT WORD PROBLEM

Does this problem represent a clearly stated computational problem?


FREQUENT WORD PROBLEM

• Genome and transcriptome assembly


• Error correction in sequence reads
• Functional analysis: transposable element identification
FREQUENT WORD PROBLEM
MODULE 3: INTRODUCTION TO BIOINFORMATICS
ALGORITHMS

• Basic algorithms

• Python Programming

• Practical sessions
WHAT IS PYTHON?

Python is a popular programming language created in 1991


It is used for:
• web development (server-side),
• software development,
• mathematics,
• system scripting.
WHAT CAN PYTHON DO?

• Python can be used on a server to create web applications.


• Python can be used alongside software to create workflows.
• Python can connect to database systems. It can also read and
modify files.
• Python can be used to handle big data and perform complex
mathematics.
• Python can be used for rapid prototyping, or for production-
ready software development.
HOW TO SETUP WORKING ENVIRONMENT WITH
PYTHON?

• Install Python: https://www.python.org


• Install Python IDE: https://www.jetbrains.com/pycharm/
• Select Community version for open-source code
• Setup working directories:
• Create a folder of your choice
• Open your folder in PyCharm
PYTHON TUTORIAL AT YOUR ALL PACE

https://www.w3schools.com/python/default.asp
https://www.learnpython.org
What should I learn here?
• From the introduction till Python Arrays in W3school
• All the Basics at LearnPython
MODULE 3: INTRODUCTION TO BIOINFORMATICS
ALGORITHMS

• Basic algorithms

• Python Programming

• Practical sessions
INTRODUCTION TO ROSALIND.INFO

http://rosalind.info/about/

• Extract real challenges of molecular biology


• Learn bioinformatics through problem solving
• Each problem is checked automatically
• Where should I start?
• Python Village track
• Bioinformatics Stronghold track

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