Bioinformatics with Python

Name: Bioinformatics with Python
Rating: 3.3 (433 reviews)

A Complete Guide For Beginners

Created byJesse E. Agbe

Last updated 9/2023

English

What you'll learn

Bioinformatics using Python
Learn Biopython and Scikit-bio
Sequence Analysis and Sequence Alignments
Write Custom Functions For DNA Sequence analysis and Protein Synthesis
Create Our Own Bioinformatics Python Package using Poetry

Course content

5 sections • 47 lectures • 13h 50m total length

Introduction and Course Plan5:02
What is Bioinformatics?5:29
bioinformatics applies biology, data, and information to solve problems using software tools; it focuses on biological data like genomics, proteomics, biomarkers, and transcriptomics through sequencing and analysis.
What is a DNA?4:52
What is Protein Synthesis?6:18
Explore how proteins form from amino acids through transcription and translation, turning DNA instructions in the nucleus into mRNA and then into amino acids at the ribosome.
Overview of Bioinformatics Databases3:11
Explore publicly accessible bioinformatics databases for sequence analysis, structure analysis, and network analysis, including SRA and PDB, to support data-driven investigations.

Handling Sequences with BioPython25:19
BioPython - Protein Synthesis18:54
BioPython - DNA Composition - GC Content,AT Content and Frequency29:11
BioPython - Sequence Alignment18:53
BioPython - Difference Between Sequence Similarity and Sequence Identity10:42
BioPython - Checking for Similarity Using Distance11:39
BioPython - Checking for Similarity Using DotPlot9:54
BioPython - Working with Biological Data File Formats - FASTA,GENBANK,etc10:57
BioPython - Working with 3D Structures14:18
BioPython - Visualizing 3D Structures8:33
BioPython - Using Nglview For 3D Structures11:56
BioPython - Using Pytraj For 3D Structure3:00
Learn to load pdb files with pytraj in python, visualize and render 3d protein structures, and display models using multiple view methods.
BioPython - BLAST4:15
Section Materials - For BioPython0:02
Real Example with BioPython - Sequence Analysis of Covid 19 DNA33:26
BioPython - Alphabets Updates6:37

Biotite - Introduction, Handling Sequences and Protein Synthesis42:16
Explore Biotite for handling DNA sequences, alphabets, and protein synthesis; learn sequence creation, transcription and translation, reverse complements, codon tables, and basic sequence analysis.
Biotite -Sequence Alignments24:22
Biotite - Working with Files9:54
learn to download genome data from Biotite, choose GenBank or FASTA formats, read and print sequences, extract annotations, and convert between formats for analysis.
Biotite - Reading Data From Bioinformatic Databases16:36
Biotite guides reading data from bioinformatic databases by performing simple and composite queries, searching nucleotide databases, fetching and downloading results, and reading byte type files in a working space.
Biotite - Fetching PDB Files from Protein Data Bank6:20
Learn to fetch PDB files from the Protein Data Bank using Biotite and a database workflow, query and download PDB formats for 3D structures, and save them locally.
Biotite - Fetching and Querying Multiple PDB Files1:49
Biotite - Working 3D Structures of Protein6:40
Biotite - Quick Overview of Phylogenetics with Biotite4:58
Biotite - Applications Subpackage11:43
Real Example with Biotite - Comparing Coronavirus and MERS viral genome54:41
Section Materials - For Biotite0:02

Scikit-Bio- Handling DNA,RNA and Protein Sequence16:48
Scikit-Bio - Protein Synthesis4:58
Scikit-Bio - DNA Composition - Checking for GC Content and AT Content10:20
Scikit-Bio - Checking for Similarity using Hamming Distance and Kmer-Distance24:06
Explains how to assess similarity between sequences using hamming distance and kmer-distance in scikit-bio. Demonstrates identifying mismatches and gaps and building custom distance functions for sequence comparisons.
Scikit-Bio - Kmers and Kmers Frequency15:22
Scikit-Bio - Sequence Alignment - Global and Local Alignments13:47
Scikit-Bio - Working with FASTA and GenBank File Formats12:23
Scikit-Bio - Phylogenetics - A Simple Overview using Newick Format11:34
Section Materials - For Scikit-Bio0:02

Bioinformatics using Custom Functions in Python1:02:42
Building A BioInformatics Package with Python -From Scratch1:16:42
Bioinformatics with NeatBio34:51
Explore building and using a bioinformatics package mbai with neatbio, covering dna, rna, protein sequences, transcription, translation, and gc content. Also learn dot plots and distance metrics for sequence comparison.
Building A Simple BioInformatics App with Streamlit58:35
Bioinformatics with Julia1:06:04
Thank You Note0:09

Requirements

Basic Understanding of Biology and Bioinformatics
Basics of Python Programming
Willingness to learn

Description

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

Who this course is for:

Beginner Python Programmers curious about doing Bioinformatics with programming
Students and Researchers
Beginners to Bioinformatics,Computational Biology and Genomics

Bioinformatics with Python

What you'll learn

Explore related topics

Course content

Module 01 - Introduction5 lectures • 25min

Module 02 - Bioinformatics with BioPython16 lectures • 3hr 38min

Module 03 - Bioinformatics with Biotite11 lectures • 2hr 59min

Module 03 - Bioinformatics with Scikit-Bio9 lectures • 1hr 49min

Module 04 - Bioinformatics Extra - Using Custom Functions, BioJulia etc6 lectures • 4hr 59min

Requirements

Description

Who this course is for: