92,913 research outputs found
Solving the Canonical Representation and Star System Problems for Proper Circular-Arc Graphs in Log-Space
We present a logspace algorithm that constructs a canonical intersection
model for a given proper circular-arc graph, where `canonical' means that
models of isomorphic graphs are equal. This implies that the recognition and
the isomorphism problems for this class of graphs are solvable in logspace. For
a broader class of concave-round graphs, that still possess (not necessarily
proper) circular-arc models, we show that those can also be constructed
canonically in logspace. As a building block for these results, we show how to
compute canonical models of circular-arc hypergraphs in logspace, which are
also known as matrices with the circular-ones property. Finally, we consider
the search version of the Star System Problem that consists in reconstructing a
graph from its closed neighborhood hypergraph. We solve it in logspace for the
classes of proper circular-arc, concave-round, and co-convex graphs.Comment: 19 pages, 3 figures, major revisio
Subclasses of Normal Helly Circular-Arc Graphs
A Helly circular-arc model M = (C,A) is a circle C together with a Helly
family \A of arcs of C. If no arc is contained in any other, then M is a proper
Helly circular-arc model, if every arc has the same length, then M is a unit
Helly circular-arc model, and if there are no two arcs covering the circle,
then M is a normal Helly circular-arc model. A Helly (resp. proper Helly, unit
Helly, normal Helly) circular-arc graph is the intersection graph of the arcs
of a Helly (resp. proper Helly, unit Helly, normal Helly) circular-arc model.
In this article we study these subclasses of Helly circular-arc graphs. We show
natural generalizations of several properties of (proper) interval graphs that
hold for some of these Helly circular-arc subclasses. Next, we describe
characterizations for the subclasses of Helly circular-arc graphs, including
forbidden induced subgraphs characterizations. These characterizations lead to
efficient algorithms for recognizing graphs within these classes. Finally, we
show how do these classes of graphs relate with straight and round digraphs.Comment: 39 pages, 13 figures. A previous version of the paper (entitled
Proper Helly Circular-Arc Graphs) appeared at WG'0
Unit Interval Editing is Fixed-Parameter Tractable
Given a graph~ and integers , , and~, the unit interval
editing problem asks whether can be transformed into a unit interval graph
by at most vertex deletions, edge deletions, and edge
additions. We give an algorithm solving this problem in time , where , and denote respectively
the numbers of vertices and edges of . Therefore, it is fixed-parameter
tractable parameterized by the total number of allowed operations.
Our algorithm implies the fixed-parameter tractability of the unit interval
edge deletion problem, for which we also present a more efficient algorithm
running in time . Another result is an -time algorithm for the unit interval vertex deletion problem,
significantly improving the algorithm of van 't Hof and Villanger, which runs
in time .Comment: An extended abstract of this paper has appeared in the proceedings of
ICALP 2015. Update: The proof of Lemma 4.2 has been completely rewritten; an
appendix is provided for a brief overview of related graph classe
Isomorphism of graph classes related to the circular-ones property
We give a linear-time algorithm that checks for isomorphism between two 0-1
matrices that obey the circular-ones property. This algorithm leads to
linear-time isomorphism algorithms for related graph classes, including Helly
circular-arc graphs, \Gamma-circular-arc graphs, proper circular-arc graphs and
convex-round graphs.Comment: 25 pages, 9 figure
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 (e.g. a de Bruijn, or a string graph),
what are all the strings that can be safely reported from 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
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