JDotter: Java Dot Plot Alignments

You will receive a warning message
when you are running this software
for the first time because these
programs will access your computer.
There is no cause of concern.
We recommend that you simply
hit the start button.
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 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. 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.

Running JDotter

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.

In addition to loading sequences in this mannor, you can load sequences and features from the POCs database from the "Plugins" menu. Select POCs from the plugins menu, and a window will open displaying sequences in the pocs database which have been previously processed. Select one from the left and one from the right and click 'open' to see the resulting dot plot.

Note: Some of the functionality of JDotter is available inside VOCs and VGO. From VOCs, it is possible to retrieve dot plots for a series of genes compared with each other. From VGO, it is possible to retrieve dot plots for whole genomes compared with each other. The JDotter client found here provides a more flexible interface for retreiving and processing plots.

JDotter Documentation

User Manual - This is the user manual for JDotter. This is also available from inside JDotter.


  1. "JDotter: A Java Interface to Multiple DotPlots Generated by Dotter"
    Ryan Brodie, Rachel L. Roper and Chris Upton (2003)
    (Accepted with Revision to Bioinformatics as an Application Note)
  2. "A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis"
    Erik L.L. Sonnhammer and Richard Durbin
    Gene 167:GC1-10 (1995)

License: GNU General Public License (GPL)

The original website of JDotter is maintained by
Dr. Chris Upton
Department of Microbiology and Biochemistry
Univeristy of Victoria
Look at http://athena.bioc.uvic.ca/pbr/jdotter/.

This version of JDotter is provided here for internal use at the IPK, Gatersleben.