Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence

Annotating protein sequences according to their biological functions is one of the key steps in understanding microbial diversity, metabolic potentials, and evolutionary histories. However, even in the best-studied prokaryotic genomes, not all proteins can be characterized by classical in vivo, in vitro, and/or in silico methods—a challenge rapidly growing alongside the advent of next-generation sequencing technologies and their enormous extension of ‘omics’ data in public databases. These so-called hypothetical proteins (HPs) represent a huge knowledge gap and hidden potential for biotechnological applications. Opportunities for leveraging the available ‘Big Data’ have recently proliferated with the use of artificial intelligence (AI). Here, we review the aims and methods of protein annotation and explain the different principles behind machine and deep learning algorithms including recent research examples, in order to assist both biologists wishing to apply AI tools in developing comprehensive genome annotations and computer scientists who want to contribute to this leading edge of biological research.