JDotter: a Java interface to multiple dotplots generated by dotter

Bioinformatics. 2004 Jan 22;20(2):279-81. doi: 10.1093/bioinformatics/btg406.


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.

Availability: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location.

Supplementary information: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Computer Graphics*
  • Database Management Systems
  • Databases, Nucleic Acid*
  • Hypermedia*
  • Information Storage and Retrieval / methods*
  • Internet
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Software
  • Systems Integration
  • User-Computer Interface*