Sequence Alignment, Scoring, and Analysis (Bioinformatics S11E1)

The theory behind Sequence alignment and sequence homology. We discuss sequence substitutions, optimal alignment strategies, BLOSUM, BLAST, and ClustalW. #Lectures @ https://dannyarends.nl/bioinformatik/ #Programming #Assignments and #Answers @ https://dannyarends.nl/bioinfo/ #Playlist:    • Bioinformatics for Plant and Animal sciences   Chapters: 00:00 Welcome back 00:10 Pairwise alignment of sequences 01:25 Global versus Local pairwise alignment 03:50 Alignments require a scoring function 04:45 Simplistic scoring function - Additive scoring with a linear gap penalty 06:28 Improving the scoring function - The affine gap penalty 09:51 DNA and Protein level alignment can vary a lot 13:08 DNA substitution probabilities, Transition versus Transversion 15:34 Amino acid substitution probabilities 17:16 The Point accepted mutation (PAM) matrix 19:05 The BLOcks SUbstitution Matrix (BLOSUM) 23:27 A fun fact about the default BLOSUM62 matrix 24:19 Differences between PAM and BLOSUM 25:52 The optimal alignment - The Smith-Waterman algorithm 28:00 Dot Plots - visualizing pairwise sequence alignments 31:19 The Basic Local Alignment Search Tool (BLAST) algorithm 33:49 Overview of different BLAST algorithms 35:23 Evaluating BLAST alignments (E-values) 36:53 Rule of thumb for sequence homology 38:13 Multiple Sequence Alignment (MSA) 41:06 Parameters affecting Multiple Sequence Alignment (MSA) 41:52 Smith-Waterman on an N-dimensional dot plot and runtime 44:04 ClustalW and real-time Multiple Sequence Alignment (MSA) 45:48 Interpreting Multiple Sequence Alignment (MSA) results 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 @   / dannyarends   This work is licensed under version 3.0 of the Creative Commons CC-BY license. For more information see http://creativecommons.org/licenses/b...