EFI - Genome Neighborhood Tool

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.

Recently-ran jobs are now listed on the first tab of the GNT. This feature is enabled the first time a new job is submitted.

When a GNN is created, the user now has the option of downloading the genomic neighborhood diagram data file; this file can be uploaded and visualized using the new "View Saved Diagrams" feature.

The user now has the option of downloading the displayed genomic neighborhood diagrams in SVG format. SVG is a vector graphics format that can be edited using Adobe Illustrator or the free InkScape editor. Those programs can be used to export publication-quality figures.

The ability to retrieve genomic neighborhood diagrams without creating and uploading an SSN is now available on the "Retrieve Neighbhorhoods" tab. It is now possible to run a BLAST against an input sequence and retrieve neighborhoods for the sequences returned by the BLAST. In addition, it is possible to submit FASTA sequences and/or files to retrieve neighborhoods for the sequences that were detected in the FASTA headers. Finally, lists of UniProt or NCBI IDs can be uploaded and neighborhoods will be retrieved for any recognized IDs.

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