Fig. 1

The result viewer page with the ‘navigate by genome’ navigation option selected. A The navigation pane gives the user the ability to navigate through the selected group of Annotations. Here, CDS 21 of phage lambda is selected. B The genome visualization depicts each feature in the selected genome at its genomic coordinates. The color of the feature is determined by the flag assigned to the annotation associated with the feature (e.g. blue for endolysin, purple for repeat region). Hovering over a feature will display information about the feature’s annotation and clicking it will navigate to that annotation. C When the ‘navigate by genome’ option is selected, users have the ability to initiate homology searches for all proteins in the selected genome. D The annotation form allows users to edit the attributes of an annotation. The history of an annotation can be displayed by clicking the “show history” button in the bottom right. E The result visualization pane allows users to select which tool and database for which they would like to view results. Proteins/domains returned from the selected search are shown as colored blocks aligned against the query sequence. The color of the block represents the statistical significance of the alignment (e.g. black for e-value 10 to light yellow for e-value 0). Clicking on a block highlights the corresponding result in the result table. Single searches are initiated from this pane. F The result table contains additional information for each hit returned by the selected homology search. The name and length of the returned subject/target are given, along with additional statistical metrics. Users can see the entire alignment in text format using the drop-down arrows. Links are available to navigate to further information about the subject/target in its native database