DNAPlotter: circular and linear interactive genome visualization

Abstract

DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages.

Availability: DNAPlotter is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/circular/

Fig. 1.

(A, B) showing Salmonella typhi genome as a circular and linear plot, respectively. The tracks from the outside represent: (1) Forward CDS; (2) Reverse CDS; (3) Pseudogenes 4. Salmonella Pathogenicity Islands (red); (5) repeat regions (blue); (6) rRNA and tRNA (green); (7) %GC plot 8. GC skew [(GC)/(G+C)]. (C) A generated example showing a transcriptome graph (black and yellow) on a circular plot for a prokaryotic genome. The tracks from the outside represent: (1) Forward CDS; (2) Reverse CDS; (3) tRNA; (4) rRNA. (D) Snapshot of the track manager showing filtering criteria.