Genome Analysis Software Info Site

Overview

In Homology Pane, if a homology search is executed using the CDS Feature as a query, the homology search results can be viewed and posted by launching the Annotation Window by right-clicking the mouse on the CDS feature.

Note

• Homology Pane is not displayed when the Annotation Window is launched by right-clicking the mouse on the main menu or the selection area on the feature map.

Display item description on Pane

• Filter operation area: A functional area for narrowing down homology search results.
• Homology Search Results List tab panel: Shows the hit subjects for homology search results. One hit is displayed per line.
• Qualifier List Panel: Lists the Qualifier values ​​described in the hit subject. The Qualifier selected (checked) here will be posted to the Query Feature.
• Toolbox: Operation button tools are arranged.

Homology search result filtering function

• You can narrow down the homology search result list by the following four items.
  • Search Database Name (Homology Site)
  • Identity Range: Specify the range of Identity in the two input fields. It is also possible to specify only one side.
  • E-value range: Specify the range of E-value in the two input fields. It is also possible to specify only one side.
  • Bit Score Range: Specify a Bit Score range in two input fields. It is also possible to specify only one side.

Operations on Homology Search Results List Tab Panel

• By clicking the Homology Search button, you can perform an additional homology analysis on the databases available for Blast search that have not yet been analyzed for homology. The execution result will be added to the list in this panel.
• Clicking on one line of Subject will move the corresponding genome map to center the subject and highlight its Feature if it is on the Reference Map.
• The checked line can be output as a CSV or FastA format file. Click the CSV… button to save the currently checked subject as a file in CSV format.
• Click the FastA… button to save the currently checked subject as a file in FastA format.
• Click the Select All button to check all subjects.
• If you click the Reverse Selected button, it will be in the opposite state to the current check state. That is, the checked subject is unchecked and the unchecked subject is checked.

Operations on the Qualifier of Subject tab panel

• The Qualifier displayed here is a Qualifier whose base range overlaps the region that was homologous to the query feature.
• Post the checked Qualifier to the query feature currently being edited on the main feature map.
• Checking the Qualifier is done manually.
• After checking all Qualifiers that need to be posted, click the Copy Qualifier button to execute the posting.