Using a Reference Database

In this exercise we will create a new project with an attached reference database and submit a reference genome to it.

Start MiGA-Web, open it in your browser and log in if necessary. Click on Create project. Enter a name (alpha-numeric characters and underscore only) for your project in the Path box. For the Type box select Genomes. Select a reference database from the pull-down menu under Reference Database. Enter optional information as you wish and click on Create new MiGA project at the bottom of the page.

On the project page, click on Upload reference datasets under Admin zone.

On the New reference datasets page, upload any one of the Pseudomonas genomes you downloaded from https://github.com/jfq3/data_sets/tree/master/Pseudomonas_genomes or one of your own.

Go to the Admin console page and turn on the daemon for the project.

Return to the project page to monitor the project progress.

Once the project has finished, click on Reference datasets on the project page. The name of your uploaded reference dataset will appear in the middle of the page, and under it will be a taxonomy annotation. Click on the genome name. In addition to the information reported for reference genomes in your previous exercises, the results page includes a Taxonomy section. This gives a statement of the closest relatives in the database, the taxonomic classification with p-values for each rank, and statements about the taxonomic novelty and genome relatedness with AAI table. The information icons and "Learn more" link lead to detailed information about each topic from the MiGA manual.