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.

Category

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.

Documentation

Online documentation

License

Public domain

Local expertise

IT: Martin Fleming

Technical Data

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