R - Monkeypox Genetics
Channel: Danny Arends
Date: 2022-05-27

Dive into the world of Monkeypox (mpox) virus research using real-world data! Learn how to analyze mpox genomics and proteomics data using the powerful R programming language. 

In this tutorial, you'll learn:
- Data Sourcing: Where to find publicly available mpox data from trusted sources like the National Center for Biotechnology Information (NCBI) and virological.org.
- Genome Analysis: How to load and work with mpox genomic sequences from FASTA files directly from NCBI.
- Building a Blast Database: Create a specialized database to compare mpox sequences for efficient analysis.
- Protein Exploration: Learn how to extract protein sequences associated with mpox using the rentrez package in R.
- Protein Consensus Model Creation: Represents common protein structures across mpox strains using Levenshtein distance and Multiple Sequence Alignment (MSA).
- Viral Genome Exploration: Blast the consensus protein sequence against the viral genome database using tblastn to identify potential interactions.
- Genomic Layout: Visualize the genomic layout of the mpox virus to understand its genetic makeup.

Access to the code used in the video! Get hands-on experience by following along with the R code available on GitHub: https://github.com/DannyArends/Monkey22

This video equips you with the skills to analyze real scientific data and contribute to ongoing research efforts.

Chapters:
00:00 Welcome
04:36 Where do we get our data from ?
08:03 Download DNA sequences from Ensembl
15:37 Committing to Github
18:20 Source IDs
32:01 Load Genome sequences from .Fasta and NCBI
39:46 Load associated protein sequences
47:54 Query proteins
50:09 Example: Chemokine binding protein
55:50 Fixing some warnings
1:01:11 Creating a protein consensus model
1:05:26 Levenstein distance
1:08:19 Multiple sequence alignment
1:10:24 TblastN the protein consensus model
1:25:54 Blast E-values explained
1:41:31 Displaying names
1:49:00 Viral variants compared
2:00:08 Viral genomic structure overview

We'll use the following R libraries: msa, RColorBrewer, rentrez, stringdist, seqinr
Blast from: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Data from: https://www.ncbi.nlm.nih.gov/ and virological.org

Thanks for taking an interest in my channel 😄If you've made it this far down, support me by giving a like or subscribing. Join me during my live stream lectures Thursday afternoons on YouTube or follow me Twitch @ https://www.twitch.tv/dannyarends

#bioinformatics  #monkeypox  #mpox #genomics  #proteomics  #rstats  #outbreak #dataanalysis