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• Introduction
• Create Whole Genome Dot Plot
• Create Whole Genome Alignment
• Create Average Nucleotide Identity Comparison
• Create Tree from Comparison
• Create Heat Map from Comparison
• Extract Multiple Sequence Alignment
• Import and export
  • Whole Genome Alignment import and export
  • Pairwise Comparison export
• Install and uninstall plugins
  • Installation of plugins
  • Uninstalling plugins
• Bibliography

Create Whole Genome Dot Plot

The Create Whole Genome Dot Plot tool makes it possible to compare two genomes and get a quick, initial overview of the similarities between them.

Note that the dot plots created by the Create Whole Genome Dot Plot are fundamentally different than the dot plots created by the Create Dot Plot tool already available in the Workbench's Toolbox (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_dot_plots.html). Whereas the classic Create Dot Plot tool compares all positions between two sequences, the Create Whole Genome Dot Plot tool works by identifying seeds, i.e., short stretches of nucleotide sequences that are shared between two genomes but not present multiple times on the same genome - which is the same approach as the one used in the initial stages of the Create Whole Genome Alignment tool. So when compared to the classic Create Dot Plot tool, the Create Whole Genome Dot Plot tool will produce less noise, but might also miss homologous regions if better matches are found in a different region on a genome.

To run the Create Whole Genome Dot Plot tool:

        Toolbox | Whole Genome Alignment () | Create Whole Genome Dot Plot ()

Once the tool wizard has opened (figure 2.1), choose two or more nucleotide sequences or nucleotide sequence lists. If the input elements are nucleotide sequence lists, each sequence in the list (chromosomes or contigs) is considered to be part of the same genome.

Figure 2.3: Select input for the Create Whole Genome Dot Plot tool.

You can set the following parameters (figure 2.2):

Figure 2.4: Configurable parameters for the Create Whole Genome Dot Plot tool.

• Minimum initial seed length The tool works by identifying seeds - short stretches that are similar - in the two genomes. This option determines the smallest number of nucleotides required before a seed is shown in the dot plot.
• Allow mismatches in seeds When this option is enabled, the search for initial seeds will allow for mismatches in the seeds. This makes it possible to visualize more divergent genome pairs, but may also introduce more noise.

The tool outputs a dot plot (figure 2.3):

Figure 2.5: Dot plot output from the Create Whole Genome Dot Plot tool.

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