MEDEA: Comparative Genomic Visualization with Adobe Flash

  1. Overview
  2. Implementation
  3. Notable Features
  4. Circular Genome Viewer
  5. Stack Map
  6. ChromoMap
  7. Dot Plot
  8. Credits
  9. Citation

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

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.

Credits

Citation

To cite your use of MEDEA, please reference http://www.broadinstitute.org/annotation/medea.


Last Updated: February 10, 2009
Contact: Reinhard Engels, Dennis Jen
medea-support@broadinstitute.org