The Department of Energy (DOE) Joint Genome Institute (JGI) is a national facility that provides DNA sequencing and analysis capabilities for bioenergy and environmental research. The JGI Genome Portal offers a unified access point to all JGI genomic databases and analytical tools. Users can search for and download genome assemblies and annotations, and interactively explore genomes and compare them with other sequenced organisms. The portal includes specialized systems for different classes of organisms, such as plants, fungi, microbes, and metagenomes. The portal also provides tools for tracking projects, accessing genome sequences and annotations, and exploring genomic data. The JGI has developed a wide array of databases and analytical systems to interpret the data, including Phytozome for plants, MycoCosm for fungi, and IMG for microbes. MycoCosm is a new integrated fungal genomics resource that provides access to over 100 fungal genomes and analytical tools for the DOE JGI Fungal Genomics program. The portal provides worldwide statistics on the usage of JGI resources and information about the latest genome releases and new tool development. The portal includes a variety of tools for genome analysis, including the Genome Browser, BLAST, and search functions. The portal also includes a community annotation system that allows users to validate and improve predicted gene models and annotations. The portal also includes functional profiles of genomes based on summaries of predicted gene annotations according to the GO, KEGG, and KOG classifications. The portal also includes tools for exploring gene families within a given group of organisms, such as the Clusters analysis tool. The portal is built on Apache HTTPD, Tomcat, and MySQL, and has a scalable database architecture. The portal is designed to handle the increasing volume of genomic data and to provide users with the tools needed to analyze and interpret this data. The JGI aims to continue to enable science and serve as a central hub for user communities by doubling sequencing and analysis throughput every year. The portal is supported by the U.S. Department of Energy and is funded to cover the open access charge.The Department of Energy (DOE) Joint Genome Institute (JGI) is a national facility that provides DNA sequencing and analysis capabilities for bioenergy and environmental research. The JGI Genome Portal offers a unified access point to all JGI genomic databases and analytical tools. Users can search for and download genome assemblies and annotations, and interactively explore genomes and compare them with other sequenced organisms. The portal includes specialized systems for different classes of organisms, such as plants, fungi, microbes, and metagenomes. The portal also provides tools for tracking projects, accessing genome sequences and annotations, and exploring genomic data. The JGI has developed a wide array of databases and analytical systems to interpret the data, including Phytozome for plants, MycoCosm for fungi, and IMG for microbes. MycoCosm is a new integrated fungal genomics resource that provides access to over 100 fungal genomes and analytical tools for the DOE JGI Fungal Genomics program. The portal provides worldwide statistics on the usage of JGI resources and information about the latest genome releases and new tool development. The portal includes a variety of tools for genome analysis, including the Genome Browser, BLAST, and search functions. The portal also includes a community annotation system that allows users to validate and improve predicted gene models and annotations. The portal also includes functional profiles of genomes based on summaries of predicted gene annotations according to the GO, KEGG, and KOG classifications. The portal also includes tools for exploring gene families within a given group of organisms, such as the Clusters analysis tool. The portal is built on Apache HTTPD, Tomcat, and MySQL, and has a scalable database architecture. The portal is designed to handle the increasing volume of genomic data and to provide users with the tools needed to analyze and interpret this data. The JGI aims to continue to enable science and serve as a central hub for user communities by doubling sequencing and analysis throughput every year. The portal is supported by the U.S. Department of Energy and is funded to cover the open access charge.