Beautifully rendered, remotely managed, securely delivered polyomic analysis.

Starting with the best Genome Browser in the cloud, period.

A Genome Browser for today

From cluttered and static...
...to beautiful and fluid.

Any old image is worth 1,000 words, but a smooth, interactive, expansive picture delivers insights like no other. Enter the Genome Profiler.

Your data should be accessible from anywhere. You should be able to view and analyze it without downloading complicated, specialized software. And it should look beautiful.

We've created a standards-compliant, mobile-device ready Genome Browser built on modern Internet technology that looks and feels like a high-performance desktop application while crawling through massive, remotely hosted datasets and annotation tracks inside your web browser.

Give it a try, and see the genome through our eyes.

High-power, low-effort infrastructure

The Genome Profiler provides managed infrastructure so you don't have to. Storage and computational resources expand and contract as you need them. And your data is accessible anywhere, any time.

Designed to integrate into high-throughput information systems, the Genome Profiler is built on a foundation of high-security and high-reliability data storage, scalable computational engines, and remotely-accessible web app interfaces.

Perform analysis, generate beautiful genome visualisations, and share them with your trusted collaborators. The Genome Profiler is built on proven Amazon Web Services infrastructure, with special attention to storing large quantities of your sensitive data and results.

Polyomic analysis and visualization for tomorrow

Starting with the best Genome Browser in the cloud is just the beginning. Because one type of data is not enough.

We are hard at work evolving our suite of apps so they help you to combine orthogonal data sources; such as sequence data, expression and copy-number arrays, pathway networks, and clinical features into a holistic view of the biological processes underlying a disease.

Using modern web browser technology to create state-of-the-art visualizations, our suite of apps will let you run pipelined analyses and then dive into the underlying results to aid understanding and explanation.

Enjoy the best Genome Browser in cloud today, and we'll let you know as we deploy new apps with novel features, functionality, capability, and visuals. Have some ideas? We'd love to talk to you about it.

Instructions

The View

When you first load the viewer, you will see a screen much like the one in the above screenshot. The top portion of the view contains the Toolbar and Minimap, the left portion contains the Names Panel, and the center portion contains the Main View.

Depending on your dataset, you will see a number of tracks displayed. Tracks can display a range of information, including features/vairants, reference sequences, coverage information, and read mappings. To turn on or off individual tracks, use the Track Settings dropdown on the left hand side of the toolbar.

Feature/Variant Tracks

Feature/Variant tracks display a feature density view when zoomed out. The track is shaded with the darker shaded regions corresponding to ares with more features.

The features will be displayed individually once the view is zoomed in, which you can do by selecting an appropriate detail type from the Zoom dropdown (on the right hand side of the toolbar). Gene features are shown as green arrows, with RNA regions overlaid in red, and CDS regions in yellow. Variant features are displayed as boxes, with Known Variants in red and variant calls from BaseSpace in grey.

Coverage track

The coverage track shows you the average number of reads mapped to each area of your genome. A scale is printed in the names panel on the left hand side. To adjust the scale of the graph, click and drag it (or tap-hold and move on a tablet).

Reference Sequence Track

The Reference Sequence Track shows you the reference sequence against which your reads are mapped. Currently the viewer supports HG18 and HG19 as reference sequences.

At low zooms the track will show a black line, but you can see the bases by selecting Bases from the zoom dropdown(on the right hand side of the toolbar). The track will initially display color coded blocks representing the bases, and then individual letters once you are sufficiently zoomed in.

Reads Track

The Reads Track is turned off by default, and does not display information at low zoom levels. To see the reads, turn on the read track in the Track Settings dropdown on the left hand side of the toolbar, and zoom in by selecting Reads from the Zoom dropdown on the left side.

Zooming

To zoom in, double tap or click the view, or use the Zoom Controls in the toolbar. If you are using an iPad or tablet, you can zoom in by pinching the main view.

Scrolling

To scroll from side to side, either swipe with yor finger (on mobile devices), or hold down the ctrl/command key and click and drag on a PC or Mac. You can also scroll by using the mouse wheel, or by using the scrollbars on a PC.

Navigation

The Navigation Dropdown (displaying "Chr1" in the screenshot above) provides some handy shortcuts for navigating around your genome.

Choose a chromosome to jump directly to that chromosome in the view. If you want to jump to a specific feature (for example a Gene or SNP), you can enter its ID in the search box. The viewer will help you by displaying a list of suggestions as you type.

The Minimap

The Minimap shows a low detail view of the entire chromosome you are viewing. It also includes a viewport marker that shows the region you are currently viewing. To jump to a particular position in the chromosome, tap it in the minimap.

Getting detailed information

When you are zoomed in far enough, the viewer will display individual features. Gene features are shown as green arrows, with RNA regions overlaid in red, and CDS regions in yellow. Variant features are displayed as boxes, with Known Variants in red and variant calls from BaseSpace in grey.

To get detailed information about any feature, just click or tap it. The information available for any particular feature is dependent on the level of research relevant to that feature, so the amount of information displayed by the viewer will vary. Most Gene features are well described, and many of the Known Variant features also have detailed descriptions.

The viewer currently provides the following information:

  • For Gene features: Information summarised from UCSC, which may include expression, structure, ortholog information and more.
  • For Known Variant features: Information summarised from dbSNP, SNPedia and OpenSNP, which may include genotype prevalence, publication information and more.
  • For Variant features (from BaseSpace analyses): Information about the variant, including basepair value of the variant (and the reference), quality information, and more.

 

System Requirements

In order to provide the best possible experience, we have initially targeted only webkit based browsers. Our supported browsers are Google Chrome and Apple Safari on the PC or Mac, and the system browsers on iPad or Android tablets. We plan to be adding support for more browsers, as well as further mobile platforms in the future. Listed below are the recommendations for all supported platforms

PC or Mac

For the fastest browsing experience, we recommend Google Chrome, but Apple Safari 5 or greater is also a good option.

iPad

Genome Profiler is supported on all iPad versions running iOS 5 or later, including the iPad Mini. For the fastest browsing experience we recommend that you use the Safari browser that came with your system, although all other browsers will still work.

Android

Genome Profiler is supported on Android Tablet devices running Android 4.0 or later. For the fastest browsing experience, we recommend Google Chrome for Android, but the Android 4.0 stock browser will also work.