Tip of the Week: DNAPlotter

dnaplotter_movieWe spend  most of our time talking about long linear genomic sequences, organized over multiple chromosomes, which are traditionally well handled by genome browsers like Ensembl, UCSC Genome Browser, GBrowse, etc.  But if you want to represent a circular genome you may prefer other graphics and views.  DNAPlotter is a tool that will enable a circular graphical representation of the data, with annotation tracks that you can customize and manage.  It can also do linear views, but for this example I’ll be illustrating a circular view.

It accepts a variety of input file format types (EMBL, GenBank, GFF3), and since it can access the files with the Artemis library tools the GMOD architecture can be used to provide the underlying database for that.  The paper explains that the Chado relational database can be used to maintain the data if you like (but that is not required).

So if you are seeking circular displays, you might want to try DNAPlotter.  You can launch a nice example from their homepage to start examining the features. This 3 minute movie examines that example and illustrates the track manager menu.

Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009 25(1):119-120; doi:10.1093/bioinformatics/btn578

Access DNAPlotter here: http://www.sanger.ac.uk/Software/Artemis/circular/