Linear-Time Recognition of Probe Interval Graphs

The interval graph for a set of intervals on a line consists of one vertex for each interval, and an edge for each intersecting pair of intervals. A probe interval graph is a variant that is motivated by an application to genomics, where the intervals are partitioned into two sets: probes and non-probes. The graph has an edge between two vertices if they intersect and at least one of them is a probe. We give a linear-time algorithm for determining whether a given graph and partition of vertices into probes and non-probes is a probe interval graph. If it is, we give a layout of intervals that proves that it is. In contrast to previous algorithms for the problem, our algorithm can determine whether the layout is uniquely constrained. This is important for the biological application, where one seeks the true layout of the intervals in a genome. As part of the algorithm we solve the consecutive-ones probe matrix problem.

• Type: Conference
• Year: 2009
• Where: ESA
• Authors: Ross M. McConnell, Yahav Nussbaum
• Keywords: Algorithm, ESA 2009, Interval Graph, Probe Interval Graph