De Bruin graphs. Part of non-compressed (a0) and compressed (a, b, c) de Bruijn graphs (k = 5). Each node contains a word (upper text of each node) and its reverse complement (lower text of each node). In the uncompressed graph, the word is a k-mer. Encircled nodes are switching with respect to red paths (pointed out by red arrows). (a0, a) Bubble due to a substitution (red letter). Starting from the forward strand in the leftmost (switching) node would generate the sequences CATCT A CGCAG (upper path) and CATCT C CGCAG (lower path). (b) Bubble due to the skipped exon GCTCG (blue sequence). This bubble is generated by the sequences CATCT ACGCA and CATCT GCTCG ACGCA. (c) Bubble due to an inexact tandem repeat. This bubble is generated by the sequences CATCT TAGGA and CATCT CATCA TAGGA, where CATCT CATCA is an inexact tandem repeat.
Sacomoto et al. BMC Bioinformatics 2012 13(Suppl 6):S5 doi:10.1186/1471-2105-13-S6-S5