MEDEA: Comparative Genomic Visualization with Adobe Flash
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Overview
You are free to deploy MEDEA components on your website as long as you credit the Broad Institute and link to this website.
As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets.
In response to this growing need, we built MEDEA, a suite of visualization tools that consists of the Circular Genome Viewer, Stack Map, ChromoMap, Dot Plot, and Viral Viewer for scientists to answer their questions.
We presented some of our work at Pecha Kucha. Please see the slides for a brief overview.
Implementation
MEDEA is written in ActionScript 3 using the Flex SDK and embedded within individual genome web sites as Flash applications. The Flash applications receive the data in JSON (JavaScript Object Notation) format, easy to read by both humans and machines. This data format will also enable users to embed MEDEA on their web sites in order to visualize their own data.
Example JSON:
[
{ "id" : "ATC1:G:7000000046786732",
"structuralFeatureType" : "Genome",
"name" : "A. cellulolyticus 11B", "sequences" : [
{ "id" : "ATC1:G:7000000046786732",
"structuralFeatures" : [
{ "stop" : 2443540,
"start":1 } ],
"name" : "A. cellulolyticus 11B",
"length" : 2443540 } ],
"sequenceType" : "Genome" }
]
Notable Features
- Full Browser Mode: Tools have the capability to utilize your entire web browser for optimized screen real estate.
- Bookmarks: Tools update their URLs to save the current view. These URLs can be bookmarked in your web browser, shared with collaborators, and acts as a history (use the back button on your web browser).
- Specialization: Tools are developed to answer specific questions and are able to communicate between each other. This fluid movement between tools utilizes the strength of each tool.
- Interactive Exploration: Tools provide an overview of the data and at the same time encourage and facilitate zooming into specific regions, while keeping the current view in context.
- Customizable: Tools offer customizable views to eliminate unwanted data and highlight regions of interest.
Circular Genome Viewer
The MEDEA Circular Genome Viewer brings together genomic feature densities and genome alignments in an overview that reflects the physical structure of circular genomes (for example, bacterial genomes and plasmids). Feature densities and alignments are represented as tracks around the circle. Tracks can be dragged and dropped into a desired position and colors are customizable.
Stack Map
The MEDEA Stack Map provides a linear view of genome features of one or more sequences. The level of detail varies from showing a zoomed out view of feature densities and a zoomed in view of stacks of feature or individual features. Selecting a region of a sequence will project the synteny between itself and displayed genomes.
ChromoMap
The MEDEA ChromoMap visualizes pre-computed genome alignments (regions of genomic similarity) between a single reference genome and one or more other genomes. The reference genome is broken up into chromosomes, each shown as a column, with alignments visualized in columns to the right.
Dot Plot
The MEDEA Dot Plot displays the synteny between a reference sequence and a number of user- selected query sequences. Sequences are displayed linearly on the x and y axes, and the synteny is represented as dot-plot lines in the center of the display. Projecting the synteny between genomes is as easy as selected dot-plot lines or sequence regions.
Viral Viewer
The MEDEA Viral Viewer displays a linear view of sequences at the nucleotide level, colored in the canonical A: red, C: blue, G: green, and T: yellow. Users submit a form on a web interface and matching sequences are displayed beneath the reference sequence. The query sequences are ordered by a phylogenetic tree displayed to the left. Selecting sequences is as easy as clicking on nodes in the tree or selecting all nodes that match a given characteristic (metadata).
Credits
- Client Software: Dennis Jen and Reinhard Engels
- Graphic Design: Christian Stolte
Citation
To cite your use of MEDEA, please reference http://www.broadinstitute.org/annotation/medea.