A dotplot compares two sequences against each other and helps identify similar regions. Using this tool, it can be determined whether a similarity between the two sequences is global (present from start to end) or local (present in patches).
To view a dotplot select two nucleotide or protein sequences in the Document Table and select Dotplot in the tab above the sequence viewer (Figure 9.1 ). If a single nucleotide or protein sequence is selected then a dot plot showing a comparison of the sequence to itself can be viewed.
The Geneious dotplot oﬀers two diﬀerent comparison engines based on the EMBOSS dottup and dotmatcher programs. You can choose which program to use by setting the sensitivity under Data Source, the panel to the right of the dot plot. The Low Sensitivity/Fast setting uses dottup, and the High Sensitivity/Slow setting uses dotmatcher. More information on these programs can be found by going to http://emboss.sourceforge.net.
The dotplot is drawn from top-left to bottom-right. The Minimap in the panel to the right of the viewer aids navigation of large dotplots by showing the overall comparison and a box indicating where the dotplot window sits.
The Colors for the Dotplot can be selected at the top of the settings panel. The Classic scheme will color the dot plot lines according to the length of the match, from blue for short matches, to red for matches over 100 bp long.
For nucleotide comparisons, the reverse complement can also be viewed, where matches with one of the sequences reverse complemented are displayed. These matches are shown by lines running from the bottom left to top right. When a pairwise alignment is selected, the path that the alignment takes through the dot plot can be displayed by checking Pairwise alignment path. This is shown as a light blue line running through the dot plot. Both of these options can be found under the Display section.
For more information on dotplots, refer to the paper by Maizel and Lenk 1981