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Bioinformatics. 2004 Jan 22;20(2):279-81.

JDotter: a Java interface to multiple dotplots generated by dotter.

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Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.


Java-Dotter (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 rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.


Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; The software is available for download from the same location.


Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page The software and source code is free for non-commercial applications.

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