Bioinformatics with Python

Course Curriculum

Chapter 1: Module 01 – Introduction

Lecture 1: Introduction and Course Plan

Lecture 2: What is Bioinformatics?

Lecture 3: What is a DNA?

Lecture 4: What is Protein Synthesis?

Lecture 5: Overview of Bioinformatics Databases

Chapter 2: Module 02 – Bioinformatics with BioPython

Lecture 1: Handling Sequences with BioPython

Lecture 2: BioPython – Protein Synthesis

Lecture 3: BioPython – DNA Composition – GC Content,AT Content and Frequency

Lecture 4: BioPython – Sequence Alignment

Lecture 5: BioPython – Difference Between Sequence Similarity and Sequence Identity

Lecture 6: BioPython – Checking for Similarity Using Distance

Lecture 7: BioPython – Checking for Similarity Using DotPlot

Lecture 8: BioPython – Working with Biological Data File Formats – FASTA,GENBANK,etc

Lecture 9: BioPython – Working with 3D Structures

Lecture 10: BioPython – Visualizing 3D Structures

Lecture 11: BioPython – Using Nglview For 3D Structures

Lecture 12: BioPython – Using Pytraj For 3D Structure

Lecture 13: BioPython – BLAST

Lecture 14: Section Materials – For BioPython

Lecture 15: Real Example with BioPython – Sequence Analysis of Covid 19 DNA

Lecture 16: BioPython – Alphabets Updates

Chapter 3: Module 03 – Bioinformatics with Biotite

Lecture 1: Biotite – Introduction, Handling Sequences and Protein Synthesis

Lecture 2: Biotite -Sequence Alignments

Lecture 3: Biotite – Working with Files

Lecture 4: Biotite – Reading Data From Bioinformatic Databases

Lecture 5: Biotite – Fetching PDB Files from Protein Data Bank

Lecture 6: Biotite – Fetching and Querying Multiple PDB Files

Lecture 7: Biotite – Working 3D Structures of Protein

Lecture 8: Biotite – Quick Overview of Phylogenetics with Biotite

Lecture 9: Biotite – Applications Subpackage

Lecture 10: Real Example with Biotite – Comparing Coronavirus and MERS viral genome

Lecture 11: Section Materials – For Biotite

Chapter 4: Module 03 – Bioinformatics with Scikit-Bio

Lecture 1: Scikit-Bio- Handling DNA,RNA and Protein Sequence

Lecture 2: Scikit-Bio – Protein Synthesis

Lecture 3: Scikit-Bio – DNA Composition – Checking for GC Content and AT Content

Lecture 4: Scikit-Bio – Checking for Similarity using Hamming Distance and Kmer-Distance

Lecture 5: Scikit-Bio – Kmers and Kmers Frequency

Lecture 6: Scikit-Bio – Sequence Alignment – Global and Local Alignments

Lecture 7: Scikit-Bio – Working with FASTA and GenBank File Formats

Lecture 8: Scikit-Bio – Phylogenetics – A Simple Overview using Newick Format

Lecture 9: Section Materials – For Scikit-Bio

Chapter 5: Module 04 – Bioinformatics Extra – Using Custom Functions, BioJulia etc

Lecture 1: Bioinformatics using Custom Functions in Python

Lecture 2: Building A BioInformatics Package with Python -From Scratch

Lecture 3: Bioinformatics with NeatBio

Lecture 4: Building A Simple BioInformatics App with Streamlit

Lecture 5: Bioinformatics with Julia

Lecture 6: Thank You Note