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DESCRIPTION VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. FEATURES VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats,(More)
Certain families of combinatorial objects admit recursive descriptions in terms of generating trees: each node of the tree corresponds to an object, and the branch leading to the node encodes the choices made in the construction of the object. Generating trees lead to a fast computation of enumeration sequences (sometimes, to explicit formulae as well) and(More)
This paper presents several randomised algorithms for generating paths in large models according to a given coverage criterion. Using methods for counting combinatorial structures, these algorithms can efficiently explore very large models, based on a graphical representation by an automaton or by a product of several automata. This new approach can be(More)
SUMMARY GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free(More)
Some strings-the texts-are assumed to be randomly generated, according to a probability model that is either a Bernoulli model or a Markov model. A rare event is the over or under-representation of a word or a set of words. The aim of this paper is twofold. First, a single word is given. We study the tail distribution of the number of its occurrences. Sharp(More)
The recursive method formalized by Nijenhuis and Wilf 15 and systematized by Flajolet, Van Cutsem and Zimmermann 8, is extended here to oating-point arithmetic. The resulting ADZ method enables one to generate decomposable data structures | both labelled or unlabelled | uniformly at random, in expected On 1+ time and space, after a preprocessing phase of On(More)
This paper addresses the problem of selecting finite test sets and automating this selection. Among these methods, some are deterministic and some are statistical. The kind of statistical testing we consider has been inspired by the work of Thevenod-Fosse and Waeselynck. There, the choice of the distribution on the input domain is guided by the structure of(More)
We used a novel graph-based approach to extract RNA tertiary motifs. We cataloged them all and clustered them using an innovative graph similarity measure. We applied our method to three widely studied structures: Haloarcula marismortui 50S (H.m 50S), Escherichia coli 50S (E. coli 50S), and Thermus thermophilus 16S (T.th 16S) RNAs. We identified 10 known(More)