EFI - Genome Neighborhood Tool
This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).
The tools are available without charge or license to both academic and commercial users.
Reorganization of UniProtKB
With the current 2026_02 release, the UniProtKB database is reorganized to include an
expanded number of Reference Proteomes to better capture biodiversity.
This includes the removal of proteins from taxonomically unclassified organisms,
i.e., those without a binomial species name (genus and species). The total number of
accessions in UniProtKB has been reduced from 253,635,358 in the “legacy” 2025_03
release to 149,810,139 in the current 2026_02 release.
We are providing the option to select either the “legacy” 2025_03 database or the
current UniProtKB database (now 2026_02) when generating SSNs. You can select the
database in the “Database” accordion on the pages for the EFI-EST options, the EFI-GNT
tool, and the Taxonomy Tool. We suggest that you compare the SSNs, GNNs, and GNDs
generated from both databases as you explore the information you are seeking.
Because the “legacy” 2025_03 release contains UniProt IDs that are no longer active
on the UniProt web site, we provide the Metadata Tool
that provides access to the node attribute metadata for the UniProt IDs in the
“legacy” 2025_03 release.
Release Notes
June 19, 2019
The genome network diagram (GND) explorer has been updated. InterPro families can now
be added as genome filters, and SwissProt annotations can be highlighted. The ability
to zoom in and out by scale (rather than genome window) is also present.
April 6, 2019
The GNT user interface has been updated. The results page contains a tab-style interface
that logically groups results on the page and allows download of SSN and GNNs without
having to scroll the page past the submission information.
December 10, 2018
Users now have the ability to regenerate GNNs from an existing GNT job (only applicable to
GNT jobs started after 12/10/2018). This allows the user to use a different neighborhood
size or cooccurrence to generate a GNN from an existing job, saving computation time.
The genomic neighborhood diagram viewer has the capability to graphically filter diagrams
by Pfam. The users can press the Ctrl button on the keyboard and click on an arrow and all
arrows with that particular family will be highlighted.
Users can now submit GNT jobs directly from the EST download page.
Previous Updates
To improve usability of the GNT, the various tools have been separated into separate tabs.
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