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- Kévin Darty, Alain Denise, Yann Ponty
- Bioinformatics
- 2009

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)

- Alain Denise, Rodica Simion
- Discrete Mathematics
- 1995

- Cyril Banderier, Philippe Flajolet, Danièle Gardy, Mireille Bousquet-Mélou, Alain Denise, Dominique Gouyou-Beauchamps
- Discrete Mathematics
- 2002

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)

- Alain Denise, Paul Zimmermann
- Theor. Comput. Sci.
- 1999

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)

- Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud
- 15th International Symposium on Software…
- 2004

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)

- Yann Ponty, Michel Termier, Alain Denise
- Bioinformatics
- 2006

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)

- Mireille Régnier, Alain Denise
- Discrete Mathematics & Theoretical Computer…
- 2004

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)

- Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, Alain Denise
- Journal of Computational Biology
- 2011

In 2004, Condon and coauthors gave a hierarchical classification of exact RNA structure prediction algorithms according to the generality of structure classes that they handle. We complete this classification by adding two recent prediction algorithms. More importantly, we precisely quantify the hierarchy by giving closed or asymptotic formulas for the… (More)

- Julien Allali, Cédric Saule, +13 authors Hélène Touzet
- Adv. Bioinformatics
- 2012

The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc… (More)