Genomic context methods: A deeper dive into how functional associations can be inferred from genomes
Channel: Lars Juhl Jensen
Date: 15/11/2021

An introduction to computational / bioinformatics approaches that allow functional associations between genes to be inferred from a collection of genomes alone. The presentation covers gene neighborhood (not limited to operon prediction), gene fusion, and phylogenetic profiling (also known as phyletic profiling) methods. Since these methods are all included in STRING, I suggest you also watch my brief introduction to the STRING database: https://youtu.be/o208DwyFbNk

0:00 Introduction: functional associations, inference from genomes, and the STRING database
0:23 Gene neighborhood: prokaryotes & operons, runs of genes, intergenic distance, evolutionary conservation, and bidirectional promoters
2:17 Gene fusion: fusion genes, fusion proteins, genome annotation errors, multiple species, and counting independent events
3:45 Phylogenetic profiling: presence/absence profiles, profile similarity, best hit profiles, redundant genomes, tree-based methods, counting independent events, lifestyle similarity, SVD-phy method, singular value decomposition (SVD), and similarity in latent space
6:25 Phylogenetic profiling example: rediscovering the cellulosome by phylogenetic profiling