Visualizing nucleotide differences across aligned bacterial genomes

Question

[Eka]

Hello all, assume a set of complete, circular bacterial genomes which differ in only a handful of SNPs or short indels. I have already aligned these genomes, so positional homology across them is established.

I would now like to visualize the positions that the SNPs are located for a publication figure. Can you recommend a software tool to me with which I can do such a visualization. I would like to demonstrate that the SNPs are located in very specific sections of the circular genome.

I would be particularly interested in a visualization method via R, which - as a Masters' student - I have recently become familiar with.

Thank you all!

[Michael G]

That's a good question. I have also wondered about an appropriate visualization tool for such cases but not found a suitable solution yet.

Answer 1

[Michael G]

I believe that DNAPlotter (which is part of the Artemis package) may be a tool for your purpose. The installation instructions for DNAPlotter are very straightforward, and there are plenty of example visualizations online to understand the capabilities of the software. The original publication of DNAPlotter is this.

However, in order to employ DNAPlotter for the purpose you are describing, you will need to convert the pairwise nucleotide differences between the aligned bacterial genomes into separate annotation tracks. Specifically, each pairwise comparison should be summarized and visualized as a different annotation track. Hence, for an alignment of four DNA sequences, there are six pairwise comparisons and, thus, six separate annotation tracks.

Please find beginner-level manuals for DNAPlotter here.