1b3445b684
multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
19 lines
1.1 KiB
Text
19 lines
1.1 KiB
Text
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.
|
|
|
|
WWW: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
|