view of a circular viral genome and its annotation

Question

[tonja.r]

I have read from bovine papillomavirus and I mapped them to the Bovine papillomavirus type 1 (ncbi JX678969.1). I would like to visualize the reference genome, my mapped reads and annotation that is provided by ncbi.

In NCBI the genome is marked as linear, however I was told that it was circular.

I tried to visualize reads and the reference via Integrative Genome Browser, but it shows the a linear genome (I need a circular) and I cannot find how I can put my annotation list, so that I see which genes are there in my genome.

Is there any tool like IGV but for circular genome where I can per hand annotate the sequence?

Answer 1

[Antonio R. Franco]

Take a look to the JAVA BRIG Ring Image Generator. It is very flexible and for sure can do what you are asking

As a standalone JAVA program, it runs in all OS

Answer 2

[rutial]

You can also try Genome Compiler: www.genomecompiler.com

It's free online and offline and works out perfect for these needs

Answer 3

[Brice Sarver]

Geneious will let you visualize circular annotated genomes. This functionality might be available in the free version (most basic manipulation and visualization is.)

Edit: I know you can visualized mapped reads against a reference designated as circular in Geneious Pro, but a license is not cheap. You might be able to do this in the free version.

Answer 4

[thackl]

You can have a look at Artemis, a slightly older genome Editor from Sanger. It reads GFF, GenBank, BAM... and performs okay for Viruses. It can produce circular maps with its DNAPlotter module quite easily.

Answer 5

[5heikki]

Circos is perhaps the best visualization tool for circular genomes, but its leaning curve is quite steep. Another option could be AngularPlasmid.