SeqMan Ultra lets you view features in text, graphical and tabular displays.

View feature information in graphical format:

You can use the Tracks panel to apply Features tracks to the Strategy and/or Alignment views, In this type of display, the feature type and name are displayed above each feature.

Hover over a feature to see a tooltip with detailed information about that feature.

An asterisk next to a feature name indicates that the feature was inferred by SeqMan NGen. For example, if you assembled data in SeqMan NGen using a template that contained a tRNA feature without a corresponding gene feature then “gene” would be inferred at that position and would be displayed as a feature in the view. However, the inferred gene would be marked with an asterisk.

View feature information in text format:

The same information in the tooltip described above can also be viewed in the Details panel. Select a feature in any view and choose View > Details.

View feature information in tabular format:

The Features view provides a table that allows you to view and manage all of the features within a selected contig. Checking and unchecking features in the view partially determines which features can be seen in the Alignment and Strategy views. (Feature display is also dependent on which tracks are visible).

To access the Features view, choose one or more contigs from the Explorer panel. Then either choose View > Features > (Contig Name) or right-click on the selected contig(s) and choose Show Feature Table.

If you select multiple contigs, a separate Features view will open for each of them. If you select “Unlocated Contigs,” individual tables will open for each member of the group. You may wish to avoid selecting “Unlocated Contigs” if you are working with a large number of such contigs, as with many transcriptome or multi-chromosome genome assemblies.

Task How To
Choose which features appear in the Features view Use the drop-down menu on the left of the Features view header to show increasingly specific tables of features: All Features, Genes (only) and the subset of feature types chosen on the Input Reference Sequences page of the SeqMan NGen wizard (e.g. CDSs and ncRNAs only).

Choose which features appear in the Strategy view To choose which features should be shown or hidden in the Strategy view when Feature tracks are displayed, add or remove checkmarks from the features in the Features view. As a shortcut, you can use any of the commands in the Features menu. For example, to show all CDS features, you could select any CDS feature in the Features view, then choose Features > Show > Show Only of Type CDS.
Add, rearrange, rename, or remove table columns Press the Change options in this view tool ( ) in the top right of the view. For instructions and a description of each column type, see Customize tables in the views.
Export data from the table Press the Export data tool ( ) in the top right of the view. This opens a save dialog in which you can save the tabular data in comma-separated (.csv) or tab-separated (.tab) format.
View features for constituent sequences Display the Features track in the Alignment or Strategy views. If you are unable to see an expected feature, it may have been on part of the sequence that was trimmed as vector.
View features on the consensus sequence Display the Features track in the Strategy view.
Simultaneously select a feature in multiple views. When you select a feature in the Features view, the range of the feature will also be selected in the Alignment view, for features on constituent sequences; or the Strategy view, for features on the consensus sequence.

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