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Bioinformatics Shared Resources

Sanford Burnham Prebys Medical Discovery Institute


Dotter 3.0 - graphical program for comparison of two sequences

Dotter is a graphical dotplot program for detailed comparison of two sequences. Here, every residue in one sequence is compared to every residue in the other sequence. The first sequence runs along the x-axis and the second sequence along the y-axis. In regions where the two sequences are similar to each other, a row of high scores will run diagonally across the dot matrix. If you're comparing a sequence against itself to find internal repeats, you'll notice that the main diagonal scores maximally, since it's the 100% perfect self-match. To make the score matrix more intelligible, the pairwise scores are averaged over a sliding window which runs diagonally. The averaged score matrix forms a three-dimensional landscape, with the two sequences in two dimensions and the height of the peaks in the third. This landscape is projected onto two dimensions by aid of greyscales - the darker grey of a peak, the higher it is. Dotter provides a tool to explore the visual appearance of this landscape, as well as a tool to examine the sequence alignment it represents.

DNA and Protein sequence analysis
Where? How?
Dotter is maintained on the emu linux server. 
Last installation and version
The latest installed version is 3.0, installed on April 19, 2002.

Online documentation
Public domain
Local expertise
IT: Martin Fleming

Technical Data

  • tested on: Linux Debian 3.0
  • emu path: /usr/local/bin