JDotter: a Java interface to multiple dotplots generated by dotter

@article{Brodie2004JDotterAJ,
  title={JDotter: a Java interface to multiple dotplots generated by dotter},
  author={Ryan Brodie and Rachel L. Roper and Chris Upton},
  journal={Bioinformatics},
  year={2004},
  volume={20 2},
  pages={
          279-81
        }
}
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… 
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References

SHOWING 1-5 OF 5 REFERENCES
Dotlet: diagonal plots in a Web browser
UNLABELLED Dotlet is a program for comparing sequences by the diagonal plot method. It is designed to be platform-independent and to run in a Web browser, thus enabling the majority of researchers to…
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
Poxvirus Orthologous Clusters: toward Defining the Minimum Essential Poxvirus Genome
TLDR
The creation of a database of continuously corrected and updated genome sequences and an easy-to-use and extremely powerful suite of software tools for the analysis of genomes, genes, and proteins is described.
Poxvirus Orthologous Clusters (POCs)
Poxvirus Orthologous Clusters (POCs) is a JAVA client-server application which accesses an updated database containing all complete poxvirus genomes; it automatically groups orthologous genes into…
“Bioinformatics” 특집을 내면서
TLDR
Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.