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Diffstat (limited to 'biology/dotter/pkg-descr')
| -rw-r--r-- | biology/dotter/pkg-descr | 19 |
1 files changed, 19 insertions, 0 deletions
diff --git a/biology/dotter/pkg-descr b/biology/dotter/pkg-descr new file mode 100644 index 000000000000..1f04ae8b9118 --- /dev/null +++ b/biology/dotter/pkg-descr @@ -0,0 +1,19 @@ +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 |