Multiple Sequence Alignment (MSA) in R  (Bioinformatics S11E2)
Channel: Danny Arends
Date: 2022-01-16

How to use the msa and seqinr R libraries to compute and visualize Pairwise and Multiple Sequence Alignments in the R programming language. R code at 29:06. This lecture is a deep dive into everything related to multiple sequence alignment: Tools, Pitfalls, Transcription Factor Binding Sites (TFBS), and Positional Weight Matrices (PWM).

Lectures @ https://dannyarends.nl/bioinformatik/
Programming Assignments and Answers @ https://dannyarends.nl/bioinfo/
Playlist: https://www.youtube.com/playlist?list=PLhR2Go-lh6X5A5WbiO3SPHuoWbwpNznUl

Chapters:
00:00 Welcome back
00:16 ClustalW 3-step alignment overview
03:30 ClustalW consensus sequence symbols
04:56 Multiple alignment pitfalls and example
06:49 Different multiple sequence alignment (MSA) tools
08:14 Future goal: Pairwise and Multiple 3D Structural Alignment
11:00 Motifs as consensus sequence and searching in DNA
12:50 String Motifs
14:27 Positional weight matrices (PWM) Motifs
15:44 Creating a Positional weight matrices (PWM) 
18:45 Future goal: Nucleotide Dependent (ND) weight matrices
20:17 Transcription Factor Binding Site (TFBS) Motif databases
21:51 Finding Motifs through phylogeny analysis
22:56 Tools overview
25:36 Multiple Sequence Alignment in denovo genome assembly
29:06 Multiple Sequence Alignment in R (install & load)
30:01 AAStringSet (or DNAStringSet) in R
31:27 ClustalW and Muscle alignment in R
32:56 The seqinr library in R to compute similarity and distances
36:07 Multiple Sequence Alignment phylogeny plot in R
40:15 Overview and end of stream

This is a live-stream recording of the MSc and PhD lecture series: Bioinformatics for plant and animal sciences, given digitally during the Covid19 pandemic at the Humboldt University in Berlin organized and lectured by Dr Danny Arends.

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 streams Thursday afternoons on Twitch @ https://www.twitch.tv/dannyarends

This work is licensed under version 3.0 of the Creative Commons CC-BY license. For more information see http://creativecommons.org/licenses/by/3.0/legalcode

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