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