Dotplot
[Menu-bar>Analyze] A dot-plot is a correlogram of two sequence .
Each dot in the pane represents a pair of residues from either
protein. The brightness of the dot is mainly determined by the
similarity of both amino acids according to the blosum62 matrix. A
number of positions up and downstream are taken into account
with declining weight.
GUI-controls:
- Slider: The width of the low pass filter with Co-sinus weights.
- Slider: The brightness of the entire plot.
- Combo box: The proteins of the X axis and Y axis.
- Toggle
: View the trace of the sequence alignment.
Anchor points:
Anchor points can be set by clicking into the pane and are marked
in the multiple sequence alignment and the scrollbar. The idea is
to chose an anchor point on a bright oblique line with high
sequence similarity. Subsequently, one can introduce gaps into the
proteins until the corresponding marks coincide in the multiple
sequence alignment pane.
Periodicity Sequence periodicity becomes evident by more than one white oblique trace. See PDB:1g61 for an example.
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Related links: 15724278 MOL_TOOLKIT:dnadot