Asymptotic wavelet and Gabor analysis: extraction of instantaneous frequencies

International audienceWe investigate the behaviour of the continuous wavelet and Gabor coefficients in the asymptotic limit, using stationary phase approximations. In particular, we show how, under some additional assumptions, these coefficients allow the extraction of some characteristics of the analysed signal, like for example frequency and amplitude modulation laws. We also briefly discuss applications to spectral lines estimations and matched filtering

Contribution of the Wigner-Ville time-frequency representation to estimate the mechanical and the thermic engine parameters on a vehicle

International audienc

Modélisation de signaux sonores par transformées temps-échelle et temps-fréquence

International audienc

FROGS: Find, Rapidly, OTUs with Galaxy Solution

International audienceMotivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.Avec le séquençage haut-débit (454, MiSeq), les pipelines de traitements de séquençage d'ARNr 16S actuels produisent de gros jeu de données. Le calcul des tables d'abondances d'OTU et leur affiliation taxonomique peinent à s'exécuter et les solutions les plus efficaces sont souvent dédiées aux spécialistes. Dans ce contexte, nous avons développé le pipeline "FROGS" : « Find Rapidly OTU with Galaxy Solution ». Développé sous environnement Galaxy, "FROGS" intègre un outil de prétraitement des données permettant le contigage de séquences, le nettoyage des données et la suppression des chimères. La déréplication des séquences se fait par un script python. L'étape de clusterisation s'effectue avec le logiciel SWARM. Un outil d'assignation retourne l’affiliation taxonomique de chaque OTU en utilisant à la fois l'algorithme RDPClassifier et NCBI blast+ sur la banque de données Silva SSU 119. Enfin, un outil de post-traitement permet aux utilisateurs de traiter la table d'abondance obtenue avec les filtres habituels, fournit des résultats statistiques et des illustrations graphiques. FROGS a été développé pour traiter de grandes quantités de données par l'utilisation d’outils innovants et une conception optimisée. De plus, il est portable sur toutes les plateformes Galaxy avec le minimum de dépendances informatiques et architecturales. FROGS a été testé sur plusieurs jeux de données simulées. L'outil se montre extrêmement rapide, robuste et hautement sensible pour la détection des OTU avec très peu de faux-positifs comparé aux autres pipelines largement utilisés par la communauté

FROGS : Find Rapidly OTU with Galaxy Solution

http://frogs.toulouse.inra.fr/il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : SOFTWAREFROGS : Find Rapidly OTU with Galaxy Solutio

Genome-wide study of structural variants in bovine Holstein, Montbéliarde and Normande dairy breeds

High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest

In grafted grapevines, physiological, transcriptional and hormonal responses to nutrient availability are strongly influenced by the rootstock genetic background

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Small indels identified with GATK and Pindel.

<p>Venn diagram summarizing small indels identified by GATK and by Pindel.</p

Breed distribution of animals used in the validation study.

<p>Table 1 summarizes the sample panel that was used for genotyping assays.</p><p>Breed distribution of animals used in the validation study.</p

Chromosomal distribution of large SVs.

<p>Histogram showing the distribution of SVs within bovine chromosomes. Deletions are shown in blue, inversions in red and tandem duplications in green.</p