What Are Some Good Interactive Circular Genome Browsers?

Question

[Burke]

Hi all,

I am looking for a interactive genome browser for circular (viral) genomes. Something that lets users view genome features in the context of the genome while allowing for backend and user customization. I need something that is interactive not simply a program to draw a static genome representation. I am familiar with a few:

• DNAplotter
• Circos
• GView and
• CGView

Are there others that I should be considering?

[Zev.Kronenberg]

Out of curiosity what genome(s)?

[Burke]

Hi Zev. You can find a description of genome here.

[Zev.Kronenberg]

LOL I know what a genome is... I was asking what kind of viral genomes you work on. I studied Microviridae.

[Burke]

LOL for sure! The current project is for papillomavirus but my previous work includes many other viruses, especially influenza virus.

[Zev.Kronenberg]

Also your link doesn't have a wiki article associated with it...

[Burke]

Corrected! Thanks!

Answer 1

[Zev.Kronenberg]

MizBee is cool, but somewhat difficult to format data for.

MizBee link

[Burke]

This looks cool, especially if someone want to do synteny visualization.

Answer 2

[Mary]

One browser strategy I thought was interesting was phiGenome. They had to accommodate both circular and linear genomes, so they have a circular map section but also have the linear view.

I know it's not exactly what you meant, but I thought it was a clever way to do it.

Example: http://www.phisite.org/main/index.php?nav=phages&nav_sel=pg&phage_id=10876.1%3B4491%3B2%3B3%3B1&ID=null&begin=begin&end=end&strand=both and use the Zoom slider to see the region change.

[Zev.Kronenberg]

Very cool. Nice reference.

[shigeta]

based on flash, no longer works too well for that reason

Answer 3

[cupton.uvic]

Our tool Viral Genome Organizer www.virology.ca/virology-ca-tools/vgo/ displays genomes as linear sequences, but might be useful depending on your needs.

Viral Genome Organizer (VGO) is an easy-to-use Java genome browser. It can be used to display information about a genome, including its genes, ORFs and start/stop codons. It can also be used to perform a regular expression search, a fuzzy motif search, and a masslist search. Because VGO talks to our database of genome sequences (VOCs) it can be used to compare genomes.

With this program, you can: view genes and predicted ORFs in one or a series of genomes. display start and stop codons within the sequence search for sequences within genomes using regular expressions; e.g GGATCC or TTTTT[ATCG]T using a fuzzy search pattern; e.g. GGATCC allowing one mismatch for genes with the highest AT composition use a GUI to select and extract regions of a genome display orthologs in a set of genomes by using the GUI to select a gene in another genome display a plot of nucleotide composition. search for the longest oligonucleotide shared between a series of unaligned genomes search the translated genome for matches to mass spec peptides graphically display data from other programs on top of the genome display

Answer 4

[Gjain]

Hi,

You might find polar histogram: pretty and useful

This previous post mentions some other options too.

[Burke]

Hi Gjain, While those are nice uses of data visualization they are not really suited for use as genome browsers. Additionally, the are static and not interactive representations. Thanks!

[Gjain]

Ahh yes, these are just meant for the static plots.

Answer 5

[madk00k]

An open-source bioinformatics toolkit UGENE provides nice interactive circular visualization of sequences.

Important features:

• large number of supported data formats for sequences and annotations
• annotations editor
• export as image or SVG

UGENE is available for Windows, Linux and MacOS.

Here is link to documentation.