Prerequisites

To execute the viewer, JavaVM (version 1.8) is required. Download at https://www.java.com/en/download/

Installation and start

To install the HSV-1 Viewer, extract the contents of the .zip-file into any folder on your computer. Navigate into that folder, where you should find three files ("run.bat", "run.command", "run.sh"; on Windows, the extensions might be hidden). To start the viewer, double-click the run-file specific for your OS.

For Windows, use "run.bat" (if the .bat-extensions are not visible, chose the file that is called a "BATCH file" or “Windows batch file” in the info column), for Mac use "run.command" and for Linux use "run.sh"

General navigation

The controls on the top of the viewer allow you to search for and navigate to specific transcripts or proteins. You can simply type in the names of individual genes or transcripts or proteins (e.g. UL41). In the main view below the controls, you will find all the information and data of the CMV genome organized in tracks. The viewer provides commonly used mechanisms to conveniently browse through the genome, including panning by holding the left mouse button and dragging, and zooming via the mouse-wheel. Moreover, double-clicking any gene or ORF centers the view on this genetic element.

Data is visualized in different tracks, where each track holds different data. This includes annotation tracks, which hold information that was manually annotated, e.g. the mRNAs and proteins, or can hold the raw data, e.g. TiSS (cRNA-seq, dRNA-seq) and Ribo-seq data. For some of the data tracks additional information is encoded by specific colors (e.g. the reading frame in the Ribo-seq data track). The color legend can be displayed by clicking the track name on the left side. Data tracks can be shown in linear or logarithmic scale. The scale for a specific track can be changed via the context-menu accessible by right-click.

Data visualization

By clicking the "Tracks"-button at the top you can open the track selector. You can then choose which data you want to display by simply selecting it or hide by simply deselecting it. The track selector is built up as a tree to organize tracks into different categories. On the highest level, there is the plus and minus strand displayed with a + and -, repsectively. For each of the two strands, you can then (de-)select the various sets of data. For example, if you want to display the cRNA-seq data, simply expand the "Transcription" category by left-clicking on the little arrow (Mac) or plus sign (Windows) left to it. Within the "TiSS" category you will find the “dRNA-seq” and “cRNA-seq” datasets for each replicate either showing all data combined (marked with a "(full)" at the end) or separately for each individual time point (by expanding the category).