Alignments of RNA structures (2009)
Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet
Abstract — We describe a theoretical unifying framework to express comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences...
Hélène Touzet, A. Chenuil, H. Touzet
Abstract The divergent domain D8 of the large ribosomal RNA is very variable and extended in vertebrates compared to other eukaryotes. We provide data from 31 species of echinoderms and present the...
Aude Liefooghe, Hélène Touzet, Jean-stéphane Varré, Lifl Umr
à grande échelle de motifs nucléiques décrits
Matthieu Defrance, Hélène Touzet, Karo Gosselin, Corinne Abbadie
Résumé. Le but de ce travail est l’analyse des régions régulatrices pour des ensembles de gènes partageant des mécanismes de régulation transcriptionnelle. Nous présentons une stratégie...
Rapport de Recherche N ° 1451 (2008)
Paris Sud, Claire Herrbach, Alain Denise, Serge Dulucq, Hélène Touzet
Alignment of RNA secondary structures using a full set of operations
Decomposition Algorithms for the Tree Edit (2008)
Distance Problem Serge, Serge Dulucq, Hélène Touzet
We study the behavior of dynamic programming methods for the tree edit distance problem, such as [5,13]. We show that those two algorithms may be described as decomposition strategies. We introduce...
Umr Cnrs Lifl, Matthieu Defrance, Hélène Touzet, Stéphane Janot
Introduction The first step toward the modelling of a transcriptional genetic network is to understand which are the transcription factors that are involved in the process. It is possible to...
MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences (2008)
Fontaine, Arnaud, De Monte, Antoine, Touzet, Hélène
MAGNOLIA is a new software for multiple alignment of nucleic acid sequences, which are recognized to be hard to align. The idea is that the multiple alignment process should be improved by taking...
Efficient and accurate P-value computation for Position Weight Matrices (2007)
Touzet, Hélène, Varré, Jean-Stéphane
Abstract Background Position Weight Matrices (PWMs) are probabilistic representations of signals in sequences. They are widely used to model approximate patterns in DNA or in protein sequences. The...
Efficient and accurate P-value computation for Position Weight Matrices (2007)
Touzet, Hélène, Varré, Jean-Stéphane
Background Position Weight Matrices (PWMs) are probabilistic representations of signals in sequences. They are widely used to model approximate patterns in DNA or in protein sequences. The usage of...
Efficient and accurate P-value computation for Position Weight Matrices (2007)
Touzet, Hélène, Varré, Jean-Stéphane
Background Position Weight Matrices (PWMs) are probabilistic representations of signals in sequences. They are widely used to model approximate patterns in DNA or in protein sequences. The usage of...
Hélène Touzet, Jean-stéphane Varré
Background: Position Weight Matrices (PWMs) are probabilistic representations of signals in sequences. They are widely used to model approximate patterns in DNA or in protein sequences. The usage of...
Defrance, Matthieu, Touzet, Hélène
Abstract Background Identifying cis -regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented transcription...
How to compare arc-annotated sequences : the alignment hierarchy (2006)
Abstract. We describe a new unifying framework to express comparison of arc-annotated sequences, which we call alignment of arc-annotated sequences. We first prove that this framework encompasses...
Team sequoia - Algorithms for large-scale sequence analysis - INRIA Activity Report (2006)
Gregory Kucherov, Hélène Touzet, Mathieu Giraud, Maude Pupin, Jean-Stéphane Varré, Laurent Noé, ...
Large Scale Matching for Position Weight Matrices (2006)
Aude Liefooghe, Hélène Touzet, Jean-stéphane Varré
Abstract. This paper addresses the problem of multiple pattern matching for motifs encoded by Position Weight Matrices. We first present an algorithm that uses a multi-index table to preprocess the...
How to detect non-coding RNAs ? (2005)
Arnaud Fontaine, Hélène Touzet
Structured non-coding RNAs have a very important functional role in the cell. They are involved in a variety of processes such as transcriptional and post-transcriptional regulation, chromosome...
A Linear Tree Edit Distance Algorithm for Similar Ordered Trees (2005)
We describe a linear algorithm for comparing two similar ordered rooted trees with node labels. The method for comparing trees is the usual tree edit distance. We show that an optimal mapping which...
CARNAC: folding families of related RNAs (2004)
Touzet, Hélène, Perriquet, Olivier
We present a tool for the prediction of conserved secondary structure elements of a family of homologous non-coding RNAs. Our method does not require any prior multiple sequence alignment. Thus, it...
Tree Edit Distance With Gaps (2003)
Helene Touzet Lifl, Hélène Touzet
this paper is to study the definition of edit distances with convex gap weights for trees. In the special case of strings, this problem has yield to the definition of classical solutions: Galil and...
Analysis of tree edit distance algorithms Serge Dulucq (2003)
And Helene Touzet, Serge Dulucq, Hélène Touzet
In this article, we study the behaviour of dynamic programming methods for the tree edit distance problem, such as [4] and [2]. We show that those two algorithms may be described in a more general...
Encoding the Hydra Battle as a rewrite system (1998)
. In rewriting theory, termination of a rewrite system by Kruskal's theorem implies a theoretical upper bound on the complexity of the system. This bound is, however, far from having been...
Université des Sciences et Technologies de Lille (1451)
Claire Herrbach, Alain Denise, Serge Dulucq, Hélène Touzet, Bât M
operations
CARNAC: folding families of related RNAs
Touzet, Hélène, Perriquet, Olivier
We present a tool for the prediction of conserved secondary structure elements of a family of homologous non-coding RNAs. Our method does not require any prior multiple sequence alignment. Thus, it...
CARNAC: folding families of related RNAs
Touzet, Hélène, Perriquet, Olivier
We present a tool for the prediction of conserved secondary structure elements of a family of homologous non-coding RNAs. Our method does not require any prior multiple sequence alignment. Thus, it...
MAGNOLIA: multiple alignment of protein–coding and structural RNA sequences
Fontaine, Arnaud, De Monte, Antoine, Touzet, Hélène
MAGNOLIA is a new software for multiple alignment of nucleic acid sequences, which are recognized to be hard to align. The idea is that the multiple alignment process should be improved by taking...