Protocol for gene annotation, prediction, and validation of genomic gene expansion

Although gene expansion plays an important role in evolution, its identification remains a challenge due to potential errors in genome assembly and annotation. Here, we describe a detailed step-by-step protocol for gene annotation, prediction of genomic gene expansion, and its computational and experimental validation. Finally, we also detail steps to discover functionality of each copy of replicated genes. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021).