Computing and counting longest paths on circular-arc graphs in polynomial time.

The longest path problem asks for a path with the largest number of vertices in a given graph. The first polynomial time algorithm (with running time O(n4)) has been recently developed for interval graphs. Even though interval and circular-arc graphs look superficially similar, they differ substantially, as circular-arc graphs are not perfect. In this paper, we prove that for every path P of a circular-arc graph G, we can appropriately “cut” the circle, such that the obtained (not induced) interval subgraph G′ of G admits a path P′ on the same vertices as P. This non-trivial result is of independent interest, as it suggests a generic reduction of a number of path problems on circular-arc graphs to the case of interval graphs with a multiplicative linear time overhead of O(n). As an application of this reduction, we present the first polynomial algorithm for the longest path problem on circular-arc graphs, which turns out to have the same running time O(n4) with the one on interval graphs, as we manage to get rid of the linear overhead of the reduction. This algorithm computes in the same time an n-approximation of the number of different vertex sets that provide a longest path; in the case where G is an interval graph, we compute the exact number. Moreover, our algorithm can be directly extended with the same running time to the case where every vertex has an arbitrary positive weight

Longest Paths in Circular Arc Graphs

As observed by Rautenbach and Sereni (arXiv:1302.5503) there is a gap in the proof of the theorem of Balister et al. (Longest paths in circular arc graphs, Combin. Probab. Comput., 13, No. 3, 311-317 (2004)), which states that the intersection of all longest paths in a connected circular arc graph is nonempty. In this paper we close this gap.Comment: 7 page

Linear-time algorithms for scattering number and Hamilton-connectivity of interval graphs.

We prove that for all inline image an interval graph is inline image-Hamilton-connected if and only if its scattering number is at most k. This complements a previously known fact that an interval graph has a nonnegative scattering number if and only if it contains a Hamilton cycle, as well as a characterization of interval graphs with positive scattering numbers in terms of the minimum size of a path cover. We also give an inline image time algorithm for computing the scattering number of an interval graph with n vertices and m edges, which improves the previously best-known inline image time bound for solving this problem. As a consequence of our two results, the maximum k for which an interval graph is k-Hamilton-connected can be computed in inline image time

Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

The longest path problem is polynomial on interval graphs.

The longest path problem is the problem of finding a path of maximum length in a graph. Polynomial solutions for this problem are known only for small classes of graphs, while it is NP-hard on general graphs, as it is a generalization of the Hamiltonian path problem. Motivated by the work of Uehara and Uno in [20], where they left the longest path problem open for the class of interval graphs, in this paper we show that the problem can be solved in polynomial time on interval graphs. The proposed algorithm runs in O(n 4) time, where n is the number of vertices of the input graph, and bases on a dynamic programming approach

Computing and Counting Longest Paths on Circular-Arc Graphs in Polynomial Time

The longest path problem asks for a path with the largest number of vertices in a given graph. The first polynomial time algorithm (with running time O(n4)) has been recently developed for interval graphs. Even though interval and circular-arc graphs look superficially similar, they differ substantially, as circular-arc graphs are not perfect. In this paper, we prove that for every path P of a circular-arc graph G, we can appropriately “cut” the circle, such that the obtained (not induced) interval subgraph G′ of G admits a path P′ on the same vertices as P. This non-trivial result is of independent interest, as it suggests a generic reduction of a number of path problems on circular-arc graphs to the case of interval graphs with a multiplicative linear time overhead of O(n). As an application of this reduction, we present the first polynomial algorithm for the longest path problem on circular-arc graphs, which turns out to have the same running time O(n4) with the one on interval graphs, as we manage to get rid of the linear overhead of the reduction. This algorithm computes in the same time an n-approximation of the number of different vertex sets that provide a longest path; in the case where G is an interval graph, we compute the exact number. Moreover, our algorithm can be directly extended with the same running time to the case where every vertex has an arbitrary positive weight