![]() ![]() Both of these options can be found under the Display section. This is shown as a light blue line running through the dot plot. ![]() ![]() When a pairwise alignment is selected, the path that the alignment takes through the dot plot can be displayed by checking Pairwise alignment path. These matches are shown by lines running from the bottom left to top right. 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.įor nucleotide comparisons, the reverse complement can also be viewed, where matches with one of the sequences reverse complemented are displayed. The Colors for the Dotplot can be selected at the top of the settings panel. 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 dotplot is drawn from top-left to bottom-right. More information on these programs can be found by going to. The Low Sensitivity/Fast setting uses dottup, and the High Sensitivity/Slow setting uses dotmatcher. You can choose which program to use by setting the sensitivity under Data Source, the panel to the right of the dot plot. The Geneious dotplot offers two different comparison engines based on the EMBOSS dottup and dotmatcher programs. A Dotplot (Self) Tab will then be visible in the Document viewer pane. If you wish to view a dotplot showing a comparison of the sequence to itself then go menu Tools → Appearance and Behavior and check the option to Show Dotplot view on single sequences (compare to self). Note that if a single nucleotide or protein sequence is selected then the dotplot tab will not be shown. To view a dotplot select two nucleotide or protein sequences in the Document Table and select Dotplot in the tab above the sequence viewer. 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). A dotplot compares two sequences against each other and helps identify similar regions. ![]()
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