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Organism Portals

Each genome sequenced at the JGI is represented by its own Organism Portal. The organism portal provides access to sequence data as well as to the set of tools available for use with this organism, such as search, BLAST alignment, functional annotation (GO, KEGG, KOG), and the Genome Browser.

At the top of each organism portal page a tab bar lists the set of tools available for exploring this organism, displayed below.

Some tools may not be available for some organisms but generally speaking, there is a suite of tools:

• Available in all portals
• Available only in Eukaryotic organism portals
• Available only in Prokaryotic organism portals

Tools available in all portals.

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 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.

Info

Assembly, project, and contact information relating to the sequencing of this organism.

Home

The front page of the organism portal, with a description of the basic biology and motivation for sequencing of the organism.

Tools available only in eukaryotic portals.

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.

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.

Clustering

The Clustering tool allows you to investigate gene-family clusters.

Synteny

The VISTA synteny application provides you with three different visualization tools for examining whole-genome DNA alignments.

Tools available only in prokaryotic portals.

Annotation

Provides a link to annotation for this microbe at Oak Ridge National Laboratories and/or JGI's Integrated Microbial Organisms (IMG) site.