Bioinformatics has become intrinsic to modern genomics research. All genomics studies, viz., structural, functional and comparative genomics research, integrate bioinformatics with experimental components. Current bioinformatics facilities and computational capabilities will enable the generation of hypotheses and stimulate the annotation and functional discoveries for new gene and genomes. The resulting experimental data from high-throughput techniques will, in turn, be further stored in databases and can be analyzed by the help of bioinformatics tools to generate more refined functional hypothesis and models that will improve the overall understanding and increase opportunities for functional genomics applications. The goal of this review is to introduce some of the important resources of bioinformatics that must be considered when planning and executing functional genomic research.