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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)

HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt età la diffusion… (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)

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)

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)

We propose a new way of automating statistical structural testing, based on the combination of uniform generation of combinatorial structures, and of randomized constraint solving techniques. More precisely, we show how to draw test cases which balance the coverage of program structures according to structural testing criteria. The control flow graph is… (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)

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)

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