title: JDotter: a Java interface to multiple dotplots generated by dotter.
abstract: 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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  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.
authors.affiliation: Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.
authors.forename: Ryan
authors.initials: R
authors.lastname: Brodie
authors.forename: Rachel L
authors.initials: RL
authors.lastname: Roper
authors.forename: Chris
authors.initials: C
authors.lastname: Upton
mesh_terms: D003196:Computer Graphics; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D019146:Hypermedia; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface