HPMV: Standalone Cartoon Tutorial

Running/Installing Standalone Interactive Cartoon

The HPMV interactive cartoon is also available as a standalone Java program. It can either be started using the Java WebStart technology () or downloaded as a jar file and run manually. Detailed running/installation help is available separately.

Overview of Standalone Interactive Cartoon

The standalone cartoon has a series of panels that can be moved through using the tabs at the bottom. In this tutorial, the initial left-to-right progression of tabs will be followed but, generally, panels may be switched to in any order.

Standalone Cartoon - highlighted tabs

Data for a set of demo proteins is embedded in the cartoon and can either be loaded using the pull-down menu or the alt-D key combination. The tutorial will briefly note the steps of loading data for a new set of proteins from the web server.

1. Loading Protein Data from the Web Server

First, use the "Genome Coords" tab to load the "GRCh38 Example" data, set the "Release" to "GRCh38, and then "Map All" the genome coordinates to protein mutations.

Standalone Cartoon - gene coordinates tab

Next, select a subset of the mapped protein mutations (blue highlight) and retrieve the feature information from the HPMV server:

Standalone Cartoon - protein mutations tab

Click anywhere on the cartoon for the "Amyloid beta A4" protein to see the detailed information (interactive cartoon):

Standalone Cartoon - all sequences tab

2. Sequence Features (Interactive Cartoon)

The "Sequence Features" tab (interactive cartoon) is shown below. Clicking on a feature in the cartoon at the top will expand and highlight the corresponding entry in the Feature Tree down at the lower left.

Click on the mutation "E191K" to show and expand the Feature Tree. Then, further expand the highlighted entry to show the detailed analysis for the E191K mutant:

Standalone Cartoon - sequence features tab - mut

Click on the "APP_N" domain and then expand and scroll the "APP_N" entry in the Feature Tree into full view:

Standalone Cartoon - sequence features - Pfam MSA entry

Click on the "Show MSA" entry and continue to the next section.

3. Multiple Sequence Alignments (MSAs)

If the previous steps (above) all worked correctly, the MSA for the APP_N domain will now be displayed. The HPMV standalone cartoon has convenient functionality to facilitate inspection of MSAs - both for the individual domain MSAs and also for the conservation MSA in the center panel.

First, click on the query (top) sequence in each alignment. The numbering for the MSA is relative to selected sequence (or to the entire MSA if nothing is selected). In this case, the numbering will now be relative to the query sequence:

Standalone Cartoon - seq ftrs - MSA seq selection

Next, use the sliders and scrollbars for each MSA to interactively compress the gaps, remove redundant sequences, and position the MSAs for convenient viewing:

Standalone Cartoon - seq ftrs - MSA sliders

Finally, use the drop-down "View" menu at the top of the window to change the MSA coloring to either "Blue" or "Heat" (showing sequence conservation):

Standalone Cartoon - seq ftrs - MSA coloring

4. PDB Structures

Clicking the 3DStruct band in the cartoon will display all structures that overlap the position that was clicked.

Click on 3ktm_A in cartoon at the top of the window, expand the corresponding entry in the Feature Tree, and then click on "Show 3D Structure":

Standalone Cartoon - seq ftrs - 3D structs - tree

The wireframe structure can be rotated by dragging the mouse. The location of the mutation(s) are shown on the structure with the original PDB numbering shown in parentheses.

Standalone Cartoon - seq ftrs - 3D structs - wireframe

5. Saving a Cartoon Image

An image of the cartoon can be saved using the drop down menu at the top of the window. The resolution can be set in terms of pixels/residue if multiple cartoons are needed all in the same scale.

Standalone Cartoon - seq ftrs - export cartoon image