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.
Important Notice

The UniProtKB database used by the EFI tools is undergoing major reorganization starting with the just-released version 2025_04 (https://www.uniprot.org/help/refprot_only_changes). When the reorganization is fully implemented (2026_02 release, Spring 2026), the number of proteins in UniProtKB will decrease from ~253M accessions in the previous 2025_03 release to ~141M accessions in the 2026_02 release.

In response to these changes, we will provide the previous 2025_03 release until the 2026_02 release is available.

The current 2025_04 release removed 82M UniProt IDs; the UniProt pages providing functional annotation for these IDs are no longer active. A new Metadata Tool provides access to the node attribute metadata for all UniProt IDs in the 2025_03 release that the tools continue to use during the UniProtKB reorganization. The Tool is available using the tab at the top of each page.

More information about the reorganization is located here.

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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