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Dotplot is a kind of graph used to compare two sequences. The two basic parameters are window size and treshold. It is a convenient and rapid method to compare long DNA or protein sequences for similarity

Software to create dot plots

  • EMBOSS contains the programs
    • dottup : word comparison
    • dotmatcher : window/threshold comparison
    • dottup : word comparison, makes n*n dotplots in one graph
  • Dotter: developed by Erik Sonnhammer and Richard Durbin (U. Stockholm, Sweden)
  • Dotlet (Java applet) at the Swiss Institute of Bioinformatics
  • Gepard (Munich Information center for Protein Sequences, Germany) : with heuristic for speeding up computation, for comparing very long sequences
  • YASS: DNA pairwise alignment tool.
  • JDotter - Originally developed for viral genomes - JAVA - Very powerful with a lot of options!
  • MUMmer - Aligning genomes, with inclusion of dotplot capabilities.
  • UGene - A complete sequence analysis platform with integrated dotplot viewer.
  • MAUVE - A GUI available for the three main OS.