TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots

We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE guarantees to find the minimum free energy structure irrespectively of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequence that can be treated but comparison with state-of-the-art algorithms shows that TT2NE is a very powerful tool within its limits. Analysis of TT2NE's wrong predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea.fr/rna/tt2ne.php

An extensive English language bibliography on graph theory and its applications, supplement 1

Graph theory and its applications - bibliography, supplement

Local Certification of Graph Decompositions and Applications to Minor-Free Classes

Local certification consists in assigning labels to the nodes of a network to certify that some given property is satisfied, in such a way that the labels can be checked locally. In the last few years, certification of graph classes received a considerable attention. The goal is to certify that a graph G belongs to a given graph class ?. Such certifications with labels of size O(log n) (where n is the size of the network) exist for trees, planar graphs and graphs embedded on surfaces. Feuilloley et al. ask if this can be extended to any class of graphs defined by a finite set of forbidden minors. In this work, we develop new decomposition tools for graph certification, and apply them to show that for every small enough minor H, H-minor-free graphs can indeed be certified with labels of size O(log n). We also show matching lower bounds using a new proof technique

Spanning trees of 3-uniform hypergraphs

Masbaum and Vaintrob's "Pfaffian matrix tree theorem" implies that counting spanning trees of a 3-uniform hypergraph (abbreviated to 3-graph) can be done in polynomial time for a class of "3-Pfaffian" 3-graphs, comparable to and related to the class of Pfaffian graphs. We prove a complexity result for recognizing a 3-Pfaffian 3-graph and describe two large classes of 3-Pfaffian 3-graphs -- one of these is given by a forbidden subgraph characterization analogous to Little's for bipartite Pfaffian graphs, and the other consists of a class of partial Steiner triple systems for which the property of being 3-Pfaffian can be reduced to the property of an associated graph being Pfaffian. We exhibit an infinite set of partial Steiner triple systems that are not 3-Pfaffian, none of which can be reduced to any other by deletion or contraction of triples. We also find some necessary or sufficient conditions for the existence of a spanning tree of a 3-graph (much more succinct than can be obtained by the currently fastest polynomial-time algorithm of Gabow and Stallmann for finding a spanning tree) and a superexponential lower bound on the number of spanning trees of a Steiner triple system.Comment: 34 pages, 9 figure