Course Description

BioInformatics with Python

Do you know that the human genomic sequence if printed out in a normal text font, would stretch for 5000 km, which is like the distance from London to Montreal, Los Angeles to Panama, Accra to Cape Town,  Tokyo to Calcutta.

This same sequence would fill about 3000 books the size of a normal book.

Understanding and analyzing this sequence is clearly going to be a huge task.

But with the advent of powerful tools and databases we can be able to grabs a simple understanding of some aspect of it.

In this introductory course we will explore the various Python tools and libraries used in analyzing DNA,RNA and genome sequence.


Hence if you are interested in analyzing large sum of biological data or are curious about DNA sequence,protein synthesis,and how vaccines are designed. Then this course is for you.


Whether you are a student or a researcher, data scientist or bioinformatics engineer,computational biologist, this course will serve as a helpful guide when doing bioinformatics in Python.

We will be exploring bioinformatics with BioPython, Biotite, Scikit-Bio, BioJulia and more.

Data is everywhere, biological data is in every living organism.Let us analyse it for useful insights


We will learn

  • how to do sequence analysis with BioPython,Biotite,etc

  • how to perform sequence alignment with code.

  • how to create our own custom functions for analyzing DNA,RNA and Proteins.

  • how to do some bioinformatics with Python.

  • how to analysis the DNA sequence of Covid 19, MERS and more.


NOTE: This is an introductory course structured like a reference material for anyone interested in doing bioinformatics with python.

Join us as we explore the world of biological data with Python

Optimizer

Jesse E. Agbe

Jesse has been a student of the bible since he got his first bible.He is an avid reader on optimization,productivity,technology.He is a student of ideas,beliefs and philosophies with a desire to see improvement and development in the lives of everyone.His driving goal is to help people to optimize standard technologies in solving certain problems as well as to grow their faith.Jesse loves questions and he is passionate about why things are the way they are and how to be efficient.He is a student,an author and a simple programmer.

Course curriculum

  • 1

    Introduction to BioInformatics

  • 2

    BioInformatics with BioPython

    • BioPython - Handling DNA,RNA and Protein Sequences

    • BioPython - Protein Synthesis

    • BioPython - DNA Composition - Checking GC and AT Content

    • BioPython- Sequence Alignment - Global and Local Alignments

    • BioPython - Checking for Sequence Similarity and Sequence Identity

    • BioPython - Checking for Similarity Using Distance (Hamming Distance)

    • BioPython - Checking For Similarity Using DotPlot

    • BioPython - Working with FASTA and GenBank File Formats

    • BioPython - Working With 3D Structures of Proteins

    • BioPython - Visualizing 3D Structures

    • BioPython - Visualizing 3D Structures Using Nglview

    • BioPython - Visualizing 3D Structure Using Pytraj

    • BioPython - Quick Overview of Blast

    • BioPython - Real Example with Covid 19 DNA Sequence

    • Section Materials For BioPython
  • 3

    BioInformatics with Biotite

    • Biotite - Introduction & Handling Sequences

    • Biotite - Global and Local Sequence Alignments

    • Biotite - Working with FASTA File formats

    • Biotite - Reading From Bioinformatics Database using Entrez

    • Biotite - Fetching Protein Data Bank (PDB) files

    • Biotite - Fetching Multiple PDB Files

      FREE PREVIEW

    • Biotite - Phylogenetics

    • Biotite- Working With 3D Structures

    • Biotite - Working with Biotite Applications

    • Biotite - Real Example Comparing Covid19 vs MERS

    • Materials For Biotite
  • 4

    BioInformatics with Scikit-Bio

    • Scikit-Bio - Handling DNA, RNA and Protein Sequences

    • Scikit-Bio - Protein Synthesis

    • Scikit-Bio - DNA-Composition- Checking GC and AT Content

    • Scikit-Bio - Kmers and Kmers Frequency of A Sequence

    • Scikit-Bio - Checking for SequenceSimilarity using Hamming Distance and Kmer Distance

    • Scikit-Bio - Sequence Alignments

    • Scikit-Bio - Working with Files

    • Scikit-Bio - Phylogenetics A simple example with Family Tree

    • Materials For Scikit-Bio Section
  • 5

    Bioinformatics -Extras

    • Creating Custom Functions For BioInformatics From Scratch

    • Converting Our Functions to A Python Package -NeatBio

    • Building A Simple BioInformatics App With Streamlit

    • Materials For BioInfo Extras