HMMs Updated February 10, 2020

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

Install Official Models

We highly recommend using the official models and annotations. It is very easy to obtain and use this data without leaving Virtool.

Go to HMM in the main navigation bar.

HHM in Main Navigation Bar

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

No HMM Data Found

Click the Install Official button to begin downloading the data. This could take some time.

Installing HMMs

When the download is complete, the data will be imported into Virtool and you can browse the annotations and use the NuVs analysis algorithm. Browse HMMs

Explore Annotations

You can browse the annotations used in NuVs results.

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

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

Click on an HMM item to view its details. Browse HMMs

Annotation Fields

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.

Find Files on Disk

The profile HMMs used by Virtool are stored in the hmm subdirectory of your Virtool data location.

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.

Go to HMM in the main navigation bar. HMM Navigation Bar

Click on Settings in the left sidebar. You should see the following: Purge in Settings

Click the Purge button. Navigating to Browse in the left sidebar should now show an HMM installation alert. No HMM Data Found