The genome sequence and protein sequence of an organism is a unique information resource that biologists have never had before. But the genome's and proteins worth, however, is determined by how well it is annotated. The purpose of process-level annotation is to understand the function of genes and their products in the context of cellular and evolutionarily conserved physiology. Recent technology advancements have made large-scale sequencing and analysis of populations in disease outbreaks, as well as large-scale diversity research aiming at broadening our understanding. A thorough method to automatic genome annotation and protein annotation is necessary to meet the challenge of timely interpretation of structure, function, and significance of this huge genetic material and its product. This book chapter informs readers on protein and genome annotation in a simple and concise manner.