Pyramid diagram: visualizing the organization of repetitive sequences in genomes.
Abstract
We introduce a new visualization method, the pyramid diagram, or pygram, capable of summarizing the hierarchical organization of repetitive structures in genome sequences. Pygrams improve over previous methods because they clearly display complex patterns of repeats located either within a single sequence or between several sequences, and are founded on the well defined notion of maximal repeat. This report describes the design and implementation of Pyramid, a tool producing pygrams, and details some applications of the visualization method in Virus and Archaea genomics.