Characterization and recognition of proper tagged probe interval graphs

TL;DR

This paper introduces a characterization and a linear-time recognition algorithm for proper tagged probe interval graphs, a subclass of probe interval graphs relevant in genomics, using new concepts like canonical sequences.

Contribution

It provides the first recognition algorithm for proper tagged probe interval graphs and introduces the canonical sequence concept for proper interval graphs.

Findings

Presented a linear-time recognition algorithm for PTPIG.

Introduced the concept of canonical sequence for proper interval graphs.

Explored the relationships between PTPIG, TPIG, and other probe interval graph classes.

Abstract

Interval graphs were used in the study of genomics by the famous molecular biologist Benzer. Later on probe interval graphs were introduced by Zhang as a generalization of interval graphs for the study of cosmid contig mapping of DNA. A tagged probe interval graph (briefly, TPIG) is motivated by similar applications to genomics, where the set of vertices is partitioned into two sets, namely, probes and nonprobes and there is an interval on the real line corresponding to each vertex. The graph has an edge between two probe vertices if their corresponding intervals intersect, has an edge between a probe vertex and a nonprobe vertex if the interval corresponding to a nonprobe vertex contains at least one end point of the interval corresponding to a probe vertex and the set of non-probe vertices is an independent set. This class of graphs have been defined nearly two decades ago, but till today there is no known recognition algorithm for it. In this paper, we consider a natural subclass of TPIG, namely, the class of proper tagged probe interval graphs (in short PTPIG). We present characterization and a linear time recognition algorithm for PTPIG. To obtain this characterization theorem we introduce a new concept called canonical sequence for proper interval graphs, which, we belief, has an independent interest in the study of proper interval graphs. Also to obtain the recognition algorithm for PTPIG, we introduce and solve a variation of consecutive $1$'s problem, namely, oriented consecutive $1$'s problem and some variations of PQ-tree algorithm. We also discuss the interrelations between the classes of PTPIG and TPIG with probe interval graphs and probe proper interval graphs.