JDotter: a Java interface to multiple dotplots generated by dotter

• Published in: Bioinformatics 2004-01, Vol.20 (2), p.279-281
• Main Authors: Brodie, Ryan, Roper, Rachel L., Upton, Chris
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Computer Graphics; Database Management Systems; Databases, Nucleic Acid; Fundamental and applied biological sciences. Psychology; General aspects; Hypermedia; Information Storage and Retrieval - methods; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software; Systems Integration; User-Computer Interface
• ISSN: 1367-4803; 1460-2059; 1367-4811
• 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.