Question: view of a circular viral genome and its annotation
1
gravatar for tonja.r
5.4 years ago by
tonja.r490
UK
tonja.r490 wrote:

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?

genome • 3.2k views
ADD COMMENTlink modified 5.3 years ago by Biostar ♦♦ 20 • written 5.4 years ago by tonja.r490
2
gravatar for rutial
5.4 years ago by
rutial40
Israel
rutial40 wrote:

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

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

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by rutial40
0
gravatar for Brice Sarver
5.4 years ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

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.

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Brice Sarver3.5k
0
gravatar for thackl
5.4 years ago by
thackl2.8k
MIT
thackl2.8k wrote:

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.

ADD COMMENTlink written 5.4 years ago by thackl2.8k
0
gravatar for 5heikki
5.4 years ago by
5heikki9.0k
Finland
5heikki9.0k wrote:

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

ADD COMMENTlink written 5.4 years ago by 5heikki9.0k
0
gravatar for Antonio R. Franco
5.4 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

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

ADD COMMENTlink written 5.4 years ago by Antonio R. Franco4.5k
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