Fig. 2

Representing DNA sequences with bidirected variation graphs. A Input DNA sequences and their reverse complements. B Generic representation of the sequences. Each node is labeled with two complementary nucleotides, from DNA strands \(+\) (upper part) and − (lower part). A node has orientation \(+1\) on a path that enters it on the left side and exits on the right side, otherwise it has orientation \(-1\). Arrows on the edges indicate the orientation of strand \(+\) of the represented sequences. The dashed arrows indicate common DNA 3-mers in the input sequences: TTG/CAA, TCG/CGA and AAC/GTT. C 3-complete and 3-faithful representation of the sequences. The quotient construction merged each pair of paths in the generic representation indicated by dashed arrows of the same color. Consequently, every 3-mer from the input sequences is represented by a unique path