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Related Experiment Videos

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

Ryan Brodie1, Rachel L Roper, Chris Upton

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

Bioinformatics (Oxford, England)
|January 22, 2004
PubMed
Summary

Java-Dotter (JDotter) provides a user-friendly Java interface for the Dotter program, simplifying the analysis of large DNA and protein sequences. This platform-independent tool enhances access to dotplot data and integrates with sequence databases for comprehensive genomic analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Dotter is a widely used program for generating dotplots of large DNA or protein sequences.
  • Laboratories often deal with numerous genomes and operate in multi-platform environments, necessitating efficient data access tools.

Purpose of the Study:

  • To develop a platform-independent Java interactive interface (JDotter) for the Linux version of the Dotter program.
  • To simplify access to dotplot data for analyzing large genomic sequences in multi-platform laboratory settings.

Main Methods:

  • JDotter operates as a client-server application.
  • It enables sending new sequences for alignment to the Dotter program.
  • It provides rapid access to a repository of preprocessed dotplots and interfaces with sequence databases or file systems for supplementary feature data.

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Main Results:

  • JDotter offers a simplified and interactive interface for Dotter.
  • It facilitates efficient analysis of large DNA and protein sequences.
  • The tool enhances data accessibility in multi-platform bioinformatics laboratories.

Conclusions:

  • JDotter significantly simplifies access to dotplot data for laboratories analyzing large genomes.
  • Its platform independence and integration capabilities make it a valuable tool for modern bioinformatics research.