Identification de gènes diagnostic chez les Rhizobium leguminosarum à l'aide de la grille informatique sous l'environnement WISDOM

Identification de gènes diagnostic chez les Rhizobium leguminosarum à l'aide de la grille informatique sous l'environnement WISDO

GTL : Une interface User-Friendly pour l'analyse de données biologique pour le Centre Jean Perrin

International audienceGTL : Une interface User-Friendly pour l'analyse de données biologique pour le Centre Jean Perri

Etude de la synthèse de matériaux inorganiques en milieu CO2 supercritique. Application à l'élaboration de membranes minérales de filtration tangentielle

MONTPELLIER-BU Sciences (341722106) / SudocALBI-ENSTIMAC (810042301) / SudocSudocFranceF

DensityMap: a genome viewer for illustrating the densities of features

Several tools are available for visualizing genomic data. Some, such as Gbrowse and Jbrowse, are very efficient for small genomic regions, but they are not suitable for entire genomes. Others, like Phenogram and CViT, can be used to visualise whole genomes, but are not designed to display very dense genomic features (eg: interspersed repeats). We have therefore developed DensityMap, a lightweight Perl program that can display the densities of several features (genes, ncRNA, cpg, etc.) along chromosomes on the scale of the whole genome. A critical advantage of DensityMap is that it uses GFF annotation files directly to compute the densities of features without needing additional information from the user. The resulting picture is readily configurable, and the colour scales used can be customized for a best fit to the data plotted.DensityMap runs on Linux architecture with few requirements so that users can easily and quickly visualize the distributions and densities of genomic features for an entire genome. The input is GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features which are used to calculate representations in density maps. In practise, DensityMap uses a tilling window to compute the density of one or more features and the number of bases covered by these features along chromosomes. The densities are represented by colour scales that can be customized to highlight critical points. DensityMap can compare the distributions of features; it calculates several chromosomal density maps in a single image, each of which describes a different genomic feature. It can also use the genome nucleotide sequence to compute and plot a density map of the GC content along chromosomes.DensityMap is a compact, easily-used tool for displaying the distribution and density of all types of genomic features within a genome. It is flexible enough to visualize the densities of several types of features in a single representation. The images produced are readily configurable and their SVG format ensures that they can be edited

The chicken repeated sequences

National audienc

Diversité des éléments génétiques mobiles dans les génomes d'iridovirus d'invertébrés

National audienc

Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

The program RepeatMasker and the database Repbase-ISB are part of the most widely used strategy for annotating repeats in animal genomes. They have been used to show that avian genomes have a lower repeat content (8–12 %) than the sequenced genomes of many vertebrate species (30–55 %). However, the efficiency of such a library-based strategies is dependent on the quality and completeness of the sequences in the database that is used. An alternative to these library based methods are methods that identify repeats de novo. These alternative methods have existed for a least a decade and may be more powerful than the library based methods. We have used an annotation strategy involving several complementary de novo tools to determine the repeat content of the model genome galGal4 (1.04 Gbp), including identifying simple sequence repeats (SSRs), tandem repeats and transposable elements (TEs). We annotated over one Gbp. of the galGal4 genome and showed that it is composed of approximately 19 % SSRs and TEs repeats. Furthermore, we estimate that the actual genome of the red jungle fowl contains about 31–35 % repeats. We find that library-based methods tend to overestimate TE diversity. These results have a major impact on the current understanding of repeats distributions throughout chromosomes in the red jungle fowl. Our results are a proof of concept of the reliability of using de novo tools to annotate repeats in large animal genomes. They have also revealed issues that will need to be resolved in order to develop gold-standard methodologies for annotating repeats in eukaryote genomes

Additional file 8: of Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

Diversity of CR1 within galGal4. The clustering of CR1 copies into subfamilies was re-investigated using SiLiX. Eight subfamilies were found, 7 of them matching with the Repbase sub-families CR1-C, CR1-D, CR1_F, CR1-G, CR1_GG, CR1-H, and CR1-Y. Their respective abundance in galGal4 was summarized in Table S2. (ODT 30 kb

Complete genome sequence of invertebrate iridovirus IIV-25 isolated from a blackfly larva

Members of the family Iridoviridae are animal viruses that infect only invertebrates and poikilothermic vertebrates. Invertebrate iridovirus 25 (IIV-25) was originally isolated from the larva of a blackfly (Simulium spp., order Diptera) found in the Ystwyth river near Aberystwyth, Wales. IIV-25 virions are icosahedral, have a diameter of ~130 nm, and contain a dsDNA genome of 204.8 kbp, with a G+C content of 30.32 %, that codes for 177 proteins. Here, we describe the complete genome sequence of this virus and its annotation. This is the fifth genome sequence of an invertebrate iridovirus reported