GMOD
SynView
Contents
Jessica Kissinger’s group at University of Georgia have contributed a very sophisticated GBrowse configuration file that creates a simple synteny viewer inside of GBrowse, which they have called SynView. This viewer is in use at PlasmoDB, and creates views like this one.
SynView is found within the GBrowse distribution, in the gbrowse/contrib/ directory. Also included in the SynView contrib directory is a GUSdb adaptor for GBrowse, but that is not required for making SynView work.
Documentation
See http://www.eupathdb.org/apps/SynView/.
Publications
Presentations
README
The files in this directory were supplied by Haiming Wang and Jessica Kissinger at University of Georgia’s Center for Tropical & Emerging Global Diseases & Department of Genetics. There are two components:
- A GUSdb adaptor (DAS::GUS) based on Bio::DB::Das::Chado in this distribution. This adaptor is written to be reasonably generic, and so it may be possible to use this as a template for creating an adaptor for any database.
- A sample configuration file (plasmodb.conf) that is similar to what drives the synteny tracks in the gbrowse installation at http://www.plasmodb.org/. For an example of what the display looks like, see http://plasmodb.org/cgi-bin/gbrowse/plasmodb/?name=Pf3D7_11_v3:380000..398999&label=Gene-Synteny
This synteny view can use any GBrowse data adaptor, including the Bio::DB::GFF and memory adaptors. Note that SynView requires Tie::IxHash.
An example dataset is also included in the MAL11 directory; this directory contains a GFF3 file, fasta file and a GBrowse configuration file set up to use the memory adaptor.
This of course is a very brief introduction to SynView, for more information, please see http://www.eupathdb.org/apps/SynView/, contact Jessica or Haiming, or see their paper in Bioinformatics:
Wang, H., Su, Y., Mackey, A., Kraemer, E., and *Kissinger, J.C.* (2006) SynView: A GBrowse-compatible Approach to Visualizing Comparative Genome Data. Bioinformatics 22(18), 2308-2309