Profile hidden Markov models (HMM) are used in Virtool to discover potential novel viruses using the NuVs workflow.

Install Official Models

1. Go to HMM in the main navigation bar

   

   If no HMM reference data has been installed, you will see the following:

   

2. Click the Install button to begin downloading the data

   It could take some time to download and install the data.

   

3. Wait for the install to complete

   When the data is ready you can browse the annotations and use the NuVs analysis algorithm.

   

Explore Annotations

You can browse the annotations used in NuVs results.

1. After HMM data has been installed, go to HMM in the main navigation bar

   

2. Use the search bar to find HMMs by annotative name (eg. RNA replicase)

3. Click on an HMM item to view its details.

   The fields in the HMM detail view describe the profile and the protein sequences that were used for its creation.

   

   Cluster	A unique integer identifier for the cluster
   Best Definitions	The three most common protein definitions found in the cluster member protein annotations.
   Length	The length of the motif identified in the profile.
   Mean Entropy
   Total Entropy
   Cluster Members	A list of the proteins included in the cluster used to construct the profile HMM.
   Families	The taxonomic families represented in the cluster and their cluster member counts. Cluster members without families are tagged None.

Purge HMM Data

It is possible to delete all HMM data from the disk and database. This is used primary during testing and development.

You will be able to reinstall the HMM data once the deletion process is complete.

1. Go to HMM in the main navigation bar

   

2. Click on Settings in the left sidebar

   

3. Click the Purge button

   You will be redirected to the HMM list view. The installation message will now be shown again because all HMM data has been deleted.