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

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

Author information

1
Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.

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.

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.

PMID:
14734323
DOI:
10.1093/bioinformatics/btg406
[Indexed for MEDLINE]

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