Protein Sequence Alignment in Theory and Practice

00:37 Sequence identity and similarity 01:39 BLOSUM62 substitution matrix 04:27 Gaps 04:49 Effects of mutations 06:35 Multiple sequence alignment 07:50 Conserved positions 08:32 ClustalOmega and WebLogo demo 10:10 Secondary structure prediction 10:51 Quick2D demo 11:46 Co-evolution and contacts 12:42 Structure prediction process We start with a non-technical introduction to the concepts of sequence identity and sequence similarity, what makes amino acids similar, and how sequence similarity relates to evolution. We continue to explaining how multiple sequence alignment can be used to understand and predict protein structure and function. The explanations are accompanied by demonstrations of sequence alignment and structure prediction using freely accessible programs on the internet. BLOSUM interactive graph: http://ahmetrasit.com/blosum/ MPI Bioinformatics Toolkit: https://toolkit.tuebingen.mpg.de/ WebLogo 3 - MSA Logo creation: https://weblogo.berkeley.edu/logo.cgi