This book provides an up-to-date review of classic and advanced bioinformatics approaches and their utility in rice research. It summarizes databases and tools for analyzing DNA, proteins and gene expression profiles, mapping genetic variations, annotation of protein and RNA molecules, phylogenetic analysis, and pathway enrichment. In addition, it presents high-throughput technologies that are widely used to provide deep insights into the genetic architecture of important traits in the rice genome. The book subsequently discusses techniques for identifying RNA-protein, DNA-protein interactions, and molecular markers, including SNP and microsatellites, in the contexts of rice breeding and genetics. Lastly, it explores various tools that are used to identify and characterize non-coding RNA in rice and their potential role in rice research.