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Overview
The JGI Genome Portal offers an interface to several bioinformatics tools for studying genomes. Major navigational relationships between the tools are shown below. For each organism sequenced by JGI, a specific subset of tools is available. Throughout a subsite for a given organism, the navigation bar provides links to the tools available for that organism.
Search
The "simple" Search tool allows you to search for InterPro domain predictions or Smith-Waterman alignments to one or more JGI-predicted genes (gene models). You can also jump to a specific JGI gene model.
Advanced Search
The Advanced Search/Annotation tool provides powerful search features such as wildcard searches, searches against homologous proteins, and iterative searches. The tool also provides links to the Genome Browser and Protein page views of results and to the locus and trancscript annotation areas.
Alignment Search (BLAST and other programs)
The BLAST tool provides an interface to NCBI's Basic Local Alignment Search Tool, BLAT and other alignment search programs for queries against JGI genomes.
The Genome Browser
JGI's Genome Browser lets you browse through JGI-predicted genes, view sequences, and study detailed alignments with nucleotide and amino acid sequences from relevant sequence databases.
The GO Browser
The Gene Ontology tool uses the Gene Ontology Consortium's controlled vocabulary for organisms to present information about JGI-predicted genes that have automatically assigned GO terms.
The KEGG Browser
The KEGG tool uses the Kyoto Encyclopedia of Genes and Genomes and its hierarchies of metabolic and regulatory pathways to present information about JGI-predicted genes that have automatically assigned KEGG terms.
The KOG Browser
The KOG tool uses euKaryotic Orthologous Groups from NCBI, a classification system based on orthologous relationships between genes in eukaryotes, to present information about JGI-predicted genes that have automatically assigned KOG identification numbers.
The Download Area
The Download feature allows you to download any available data related to a given organism including assembled genomes, gene models, predicted protein files, ESTs, and transcripts.