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PubMed · 14734323

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

Ryan Brodie·Rachel L Roper·Chris Upton
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Abstract

UNLABELLED: 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.

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Computer GraphicsDatabase Management SystemsDatabases, Nucleic AcidHypermediaInformation Storage and RetrievalInternetSequence AlignmentSequence Analysis, DNASoftwareSystems IntegrationUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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Ryan Brodie, Rachel L Roper, Chris Upton. 2004-01-22. JDotter: a Java interface to multiple dotplots generated by dotter.. https://doi.org/10.1093/bioinformatics%2Fbtg406

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