Physical Mapping is a central problem in molecular biology ... and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NP-complete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the k-consecutive ones problem for k >= 2. These models have been chosen to reflect various features typical in biological data, including false negative and positive errors, small width of the map and chimericism.

The Physical Mapping Problem is to reconstruct the relative position of fragments (clones) of DNA along the genome from information on their pairwise overlaps. We show that two simplified versions of the problem belong to the class of NP-complete problems, which are conjectured to be computationally intractable. In one version all clones have equal length, and in another, clone lengths may be arbitrary. The proof uses tools from graph theory and complexity.

. A common method for drawing directed graphs is, as a first step, to partition the vertices into a set of k levels and then, as a second step, to permute the vertices within the levels such that the number of crossings is minimized. We suggest an alternative method for the second step, namely, removing the minimal number of edges such that the resulting graph is k-level planar. For the final diagram the removed edges are reinserted into a k-level planar drawing. Hence, instead of considering the k-level crossing minimization problem, we suggest solving the k-level planarization problem. In this paper we address the case k = 2. First, we give a motivation for our approach. Then, we address the problem of extracting a 2-level planar subgraph of maximum weight in a given 2-level graph. This problem is NP-hard. Based on a characterization of 2-level planar graphs, we give an integer linear programming formulation for the 2-level planarization problem. Moreover, we define and investigate t...

We consider graph drawings in which vertices are assigned to layers and edges are drawn as straight line-segments between vertices on adjacent layers. We prove that graphs admitting crossing-free h-layer drawings (for fixed h) have bounded pathwidth. We then use a path decomposition as the basis for a linear-time algorithm to decide if a graph has a crossing-free h-layer drawing (for fixed h). This algorithm is extended to solve a large number of related problems, including allowing at most k crossings, or removing at most r edges to leave a crossing-free drawing (for fixed k or r). If the number of crossings or deleted edges is a non-fixed parameter then these problems are NP-complete. For each setting, we can also permit downward drawings of directed graphs and drawings in which edges may span multiple layers, in which case the total span or the maximum span of edges can be minimized. In contrast to the so-called Sugiyama method for layered graph drawing, our algorithms do not assume a preassignment of the vertices to layers.

) S. Muthukrishnan Laxmi Parida y Abstract We initiate the complexity study of physical mapping with the emerging technology of Optical Mapping (OM) pioneered by the team lead by David Schwartz at the W. M. Keck Laboratory for Biomolecular Imaging, Dept of Chemistry, NYU. In currently popular electrophoretic approaches, information about the relative ordering of the fragments comprising the DNA molecule is lost, thus leading to difficult computational problems of composing the fragments in to a physical map depicting their relative order. In contrast, the relative ordering of the pieces is readily obtained in OM. However, OM faces serious technological challenges as it has low resolution and is faultprone. We take a combinatorial approach to the problem of constructing physical maps from the erroneous data generated by OM. We identify two abstract problems in this context, namely, the Exclusive Binary Flip-Cut and Exclusive Weighted Flip-Cut problems. For both, we present polynom...

The determination of the sequence of all nucleotide base-pairs in a DNA molecule, from restriction-fragment data, is a complex task and can be posed as the problem of finding the optima of a multi-modal function. A genetic algorithm that uses multi-niche crowding permits us to do this. Performance of this algorithm is first tested using a standard suite of test functions. The algorithm is next tested using two data sets obtained from the Human Genome Project at the Lawrence Livermore National Laboratory. The new method holds promise in automating the sequencing computations.

A bipartite graph is biplanar if the vertices can be placed on two parallel lines (layers) in the plane such that there are no edge crossings when edges are drawn straight. The 2-Layer Planarization problem asks if k edges can be deleted from a given graph G so that the remaining graph is biplanar. This problem is NP-complete, as is the 1-Layer Planarization problem in which the permutation of the vertices in one layer is fixed. We give the following fixed parameter tractability results: an O(k ·6 k +|G|) algorithm for 2-Layer Planarization and an O(3 k ·|G|) algorithm for 1-Layer Planarization, thus achieving linear time for fixed k.

We give an O(ϕ k · n 2) fixed parameter tractable algorithm for the 1-SIDED CROSSING MINIMIZATION problem. The constant ϕ in the running time is the golden ratio ϕ = (1 + √ 5)/2 ≈ 1.618. The constant k is the parameter of the problem: the number of allowed edge crossings.

. Practical applications, like radio frequency assignments, led to the denition of disk intersection graphs in the plane, called shortly disk graphs. If the disks in the representation are not allowed to overlap, we speak about disk contact graphs (coin graphs). In this paper we survey recognition-complexity results for disk intersection and contact graphs in the plane. In particular, we refer a classical result by Koebe about disk contact representations, and works of Breu and Kirkpatrick about bounded-ratio disk representations. We prove that the recognition of disk-intersection graphs (in the unbounded ratio case) is NP-hard. This result is proved in a more general setting of noncrossing arc-connected sets. We also show some partial results concerning recognition of ball intersection and contact graphs in higher dimensions. In particular, we prove that the recognition of unit-ball contact graphs is NP-hard in dimensions 3; 4, and 8 (24). 1 Introduction 1.1 Intersect...

An h-layer drawing of a graph G is a planar drawing of G in which each vertex is placed on one of h parallel lines and each edge is drawn as a straight line between its end-vertices. In such a drawing, we say that an edge is proper if its endpoints lie on adjacent layers, flat if they lie on the same layer and long otherwise. Thus, a proper h-layer drawing contains only proper edges, a short h-layer drawing contains no long edges, an upright h-layer drawing contains no flat edges, and an unconstrained h-layer drawing contains any type of edge. We prove