From VGO, it is possible to retrieve dot plots for whole genomes compared with each other. License: GNU General Public License (GPL) The original website of JDotter is maintained by Dr.The JDotter client found here provides a more flexible interface for retreiving and processing plots. Chris Upton Department of Microbiology and Biochemistry Univeristy of Victoria Look at

You will receive a warning message when you are running this software for the first time because these programs will access your computer. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as access a repository of preprocessed dotplots.

For more infomation please read About Warnings Dialog JDotter is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences.

JDotter also interfaces with a sequence feature database or file system to be able to display supplementary feature data.

With these functions, together with its platform independence, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.

1) Ensure Java Web Start v 1.0.1 is installed on your machine 2) Click the "Launch" button, or the JDotter icon to open JDotter (above) 3) See the "Help" menu for the JDotter manual 4) To exit, choose "Quit" from the file menu Quick Start: To launch JDotter, click the launch button above.

Once the JDotter window has appeared, you may choose to enter your own sequences interactively in the spaces provided.To add a sequence to the list to submit, select "Add Sequence".You may view the current list by clicking "View Submission".From here you can select and remove any sequences you choose not to submit.Once all seequences have been added, click "Submit" and a request will be made to the dotter server to process the request.This may take a few seconds to complete as dot plots can be quite large.