- Navigate to track
- Display feature info
- Edit features attributes
- Genes context menu
- Download the gene table data
Genes panel displays a list of genes/transcripts/exons and other features of the current dataset (from corresponding GFF/GTF and GenBank files) in a tabular view.
To navigate to a feature, click the certain feature row in the Genes table. This feature will be opened in the "Browser" panel, at the GENE track, e.g.:
The GENE track will be auto zoomed so that the selected feature appears at the full size and approximately at the center of the track's visible part.
To view the info details about the certain feature, click the Info button in the row of that feature in the Genes table, e.g.:
The info pop-up contains all feature info:
- mandatory fields with their values from the corresponding columns of the origin gene files (shown as is)
- additional attributes with their values from the "Attributes" column of the origin gene file (shown with the
ATTRlabel) - Sequence field with a feature nucleotide sequence
Users can modify gene/feature attributes shown in the Genes panel via the GUI.
These changes will be saved in NGB and will be available to all other users, but they don't touch the original GENE files.
Details:
- user can modify the attribute values manually for any gene/feature from the GENES panel
- all field values can be changed, no matter the type attribute has - mandatory or optional/additional (except "Chromosome", "Start", "End")
- user can add a new attribute and specify a value for it to the feature. Such attribute will be shown as additional and marked with the
ATTRlabel - user can remove any additional attribute from the feature (mandatory fields can not be removed)
- modified/created/deleted attributes don't affect the original GENE files. All changes are being done only in the inner NGB database
Modifying attributes is being performed via the Info pop-up of the gene/feature - click the Info button in the row of the desired feature in the Genes table, then click the Edit button, e.g.:
The modifying regimen will be enabled:
All fields that values can be modified are displayed with the underline.
To change such value - click it and specify a new one, e.g.:
To remove the attribute with its value - click the minus button near the attribute, e.g.:
This attribute will disappear from the list.
To add a new attribute - click the Add button under the list. Two fields will appear - left one for the attribute name and the right one for the attribute value, e.g.:
Both fields should be filled in for a new attribute (empty values are not allowed), e.g.:
To add another attribute - click the Add button again.
Once all changes are done - click the Save button:
Changes will be saved:
You can check it at the Genes panel as well:
User can view all changes that were performed with the certain feature attributes - what was changed, when and by whom.
It can be done via the History tab in the feature Info pop-up:
Here the list of performed actions is displayed.
Each action record in the list contains:
- username who performed changes
- date and time of changes
- details of changing (names of the changed attributes, their old and new values)
History is being sorted by date - from the newest to older events.
Users can use the context menu from the Genes table for the quick access to some additional functionality. To open the context menu, click the right mouse button on a feture row, e.g.:
From here, user can for the current feature:
- open the BLAST search
- open a visualized 3D protein structure in the Molecular viewer
- open the Homologs search
Note: not all context menu items are available for all features. In case of some restrictions, the corresponding warning message will be shown, e.g.:
To download the data displayed in the Genes table - click the download icon in the panel header.
The pop-up will appear:
Here:
- select the format for the downloading table data (CSV or TSV, CSV by default)
- set the checkbox if the the header should be included to the downloading file (header is not included by default)
Once the setup is finished, click the Download button. Table will be downloaded automatically:
The downloaded table will contain only the same data that was displayed in the Genes table before the download (considering all filters and sortings):
