A reference sequence database is chosen as the basis by which query sequences are annotated, and therefore, must include annotated reference sequences. These reference sequences will be used by the pipelines to automatically annotate your input sequences based on the criteria specified in the selected scaffold and pipeline.
Reference sequence database can only be created by admin users. This involves the following steps:
- Select Reference sequence under Organization databases, located in the Navigation panel.
- Click on the menu button (vertical ellipsis) or New database in the Menu bar to create a new database and provide a name. A new empty database will be created.
- Add annotated sequences in Genbank or Geneious formats to the newly created database by dragging and dropping or using the Upload button in the Menu bar. You can add both individual sequences or multi-sequence files (sequence list). The latter will show as a single entry in the database.
Note that files cannot be uploaded directly to the Sequence reference database root - you must first create a new database to add your files to.
The human and mouse immunoglobulin are bundled with Geneious Biologics but custom reference sequences can be used as well. To learn more about custom reference sequences and how to set up a database using custom reference sequences, please refer to the following article.