Interactive Filtering
The mouse can be used to select families to filter. To
do this, press and hold the Ctrl key on the keyboard
and click on a protein. All of the PFam families that
are associated with the protein will be highlighted.
Viewing Metadata
Moving the mouse over a specific protein will show a
popup box containing metadata. As soon as the mouse is
moved away from the protein, the box disappears. To
keep the box open, click on the protein, and the box
will remain visible until the mouse is moved over a
different protein.
Copying Metadata
Clicking the copy
icon when
the metadata popup box is visible will copy the
metadata to the clipboard. This information can be
pasted into another document for further use.
Direct Link to UniProt Data
The UniProt ID in the metadata popup box is a link that
can be used to access the UniProt website for the given protein.
Changing the Window (Scale)
By default a maximum of 40 kbp are shown. This window
scale factor can be increased
or
decreased
by using the zoom buttons. All
visible diagrams wil be reloaded when using the zoom
buttons.
Changing the Window (Gene)
The GND explorer can display from 1 to 20 genes on
either side of the query gene (center, red). This can be
changed by clicking the "genes" drop down menu in the
Genome Window section, and clicking the Apply button.
Updating the Filter Legend
Selecting a family filter makes that family, along with its
assigned color, appear in a legend box below the "Clear Filter"
button. Individual families can be removed from the legend
by moving the mouse over the color box and pressing the X
button that appears in the color box. For InterPro
families, the color is not assigned, but the functionality
is the same.
Data Export
It is possible to export a file that provides the data used to generate the diagrams.
The data file format is SQLite, and it can be uploaded to the EFI-GNT
tool and viewed again in the future via the
View Saved Diagrams
option.
For advanced use, the file can also be opened with
DB Browser for SQLite
to manually extract data.
The currently displayed diagrams can be exported to the Gene Graphics
format and displayed using the
Gene Graphics
comparative genomics visualization tool.
