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Dot plots
Dot plots provide a powerful visual comparison of two sequences. Dot plots can also be used to compare two regions of similarity within a sequence of DNA or protein. Each axis of the plot represents the sequence. If a sequence is found between the two axis, a dot is drawn. This results in a diagonal line if two identical sequences are plotted against each other. This can also be used to find repeats within a sequence of interest.
After choosing which DNA(s) or protein(s) to compare, the following parameters are set:
- Distance correction (only applicable for protein sequences) In order to treat evolutionary transitions of amino acids, a distance correction measure can be used when calculating the dot plot. The distance correction matrices take into account the likeliness of one amino acid changing to another. Available distance matrices:
- BLOSUM45
- BLOSUM62
- BLOSUM80
- PAM30
- PAM60
- Window size A residue by residue comparison would result in a lot of similarities because of a low number of different residues and therefore of course also in a very noisy background. Moreover, a residue by residue comparison can be very time consuming and computationally demanding. Increasing the window size will make the dot plot “smoother” to operate.
When viewing a dot plot, the usual CLC workbench maneuvering actions are available:
- Zoom in
- Zoom out
- Move around within a zoomed area
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