Section: New Results

Cross-fertilising different computational approaches and other theoretical results

Bubble generator.

As mentioned earlier, a theoretical recent work of the team related to NGS analysis was accepted at the 43rd International Workshop on Graph-Theoretic Concepts in Computer Science (WG) in 2017 [30]. It introduced what was called a bubble generator.

Bubbles are pairs of internally vertex-disjoint (s, t)-paths with applications in the processing of DNA and RNA data. For example, enumerating alternative splicing events in a reference-free context can be done by enumerating all bubbles in a de Bruijn graph built from RNA-seq reads. However, listing and analysing all bubbles in a given graph is usually unfeasible in practice, due to the exponential number of bubbles present in real data graphs. In [30], we proposed a notion of a bubble generator set, i.e. a polynomial-sized subset of bubbles from which all the others can be obtained through the application of a specific symmetric difference operator. This set provides a compact representation of the bubble space of a graph, which can be useful in practice since some pertinent information about all the bubbles can be more conveniently extracted from this compact set. Furthermore, we provide a polynomial-time algorithm to decompose any bubble of a graph into the bubbles of such a generator in a tree-like fashion.