Integrative Transcriptomics

GenomeRing: alignment visualization based on SuperGenome coordinates

With GenomeRing we present two complementary approaches to tackle the problem of quick and comprehensive interpretation of all important genomic variations together with various supplemental data. Our SuperGenome concept allows for the computation of a common coordinate system for all genomes in a multiple alignment. This enables the consistent placement of genome annotations in the presence of insertions, deletions, and rearrangements. The SuperGenome concept comes with our GenomeRing visualization which, based on the SuperGenome, creates an interactive plot of the multiple genome alignment in a circular layout.

 

 

Example for the GenomeRing Visualization for 4 Campylobacter jejuni strains.
Example for the GenomeRing Visualization for 4 Campylobacter jejuni strains.

Citation

If you use GenomeRing, please cite:
Herbig A, Jäger G, Battke F, Nieselt K.
 GenomeRing: alignment visualization based on SuperGenome coordinates, Bioinformatics 2012, 28(12):i7-i15.

Using GenomeRing

There are two possibilities to use GenomeRing:

  1. As a stand-alone Java FX version. You need at least Java 11 to use this version. For use of the stand-alone version, basically follow the instructions below.
     
  2. GenomeRing is integrated into Mayday.
    After starting Mayday, you can open GenomeRing with an example alignment via the “Mayday” menu.

    You can start Mayday directly from here.

Material

For information on how to use Mayday’s core features, please refer to the tutorials and how-to documents listed on the Mayday page.

We provide an example dataset with a step-by-step guide to recreate the Campylobacter analysis presented in our manuscript.

  1. Start the JavaFX version of GenomeRing or the version integrated into Mayday
  2. Download one of the SuperGenome alignment files (we recommend to load the original xmfa file and to set the minimal block size in Mayday)
    1. precomputed for minimal block size 10000:
      Campylobacter_jejuni_10000.blocks
    2. precomputed for minimal block size 7500:
      Campylobacter_jejuni_7500.blocks
    3. precomputed for minimal block size 5000:
      Campylobacter_jejuni_5000.blocks
    4. original XMFA alignment file with 4 genomes (SuperGenome will be generated in Mayday): Cjejuni.xmfa
  3. Download the additional dataset Campylobacter_jejuni.maydayz
  4. Follow the steps in the step-by-step guide