CompaGB: An open framework for genome browsers comparison

<p>Abstract</p> <p>Background</p> <p>Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming.</p> <p>Findings</p> <p>To assist in this task, we propose a community-based framework based on two cornerstones: (i) the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile) with features of interest to a community-based framework: easy management of evolving data, user comments...</p> <p>Conclusions</p> <p>The framework is available at <url>http://genome.jouy.inra.fr/CompaGB</url>. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1) choose a genome browser that would better fit their particular project, (2) visualize features comparatively with easily accessible formats, such as tables or radar plots and (3) perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology. A summary of the features of the compared genome browsers is presented and discussed.</p

Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

BACKGROUND: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. RESULTS: Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. CONCLUSION: The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL:

Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

International audienc

Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes

<p>Abstract</p> <p>Background</p> <p>The basidiomycete fungus <it>Microbotryum violaceum </it>is responsible for the anther-smut disease in many plants of the Caryophyllaceae family and is a model in genetics and evolutionary biology. Infection is initiated by dikaryotic hyphae produced after the conjugation of two haploid sporidia of opposite mating type. This study describes <it>M. violaceum </it>ESTs corresponding to nuclear genes expressed during conjugation and early hyphal production.</p> <p>Results</p> <p>A normalized cDNA library generated 24,128 sequences, which were assembled into 7,765 unique genes; 25.2% of them displayed significant similarity to annotated proteins from other organisms, 74.3% a weak similarity to the same set of known proteins, and 0.5% were orphans. We identified putative pheromone receptors and genes that in other fungi are involved in the mating process. We also identified many sequences similar to genes known to be involved in pathogenicity in other fungi. The <it>M. violaceum </it>EST database, MICROBASE, is available on the Web and provides access to the sequences, assembled contigs, annotations and programs to compare similarities against MICROBASE.</p> <p>Conclusion</p> <p>This study provides a basis for cloning the mating type locus, for further investigation of pathogenicity genes in the anther smut fungi, and for comparative genomics.</p

MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level

BACKGROUND: The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. DESCRIPTION: Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. CONCLUSION: The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic

Structuration d'un flot de conception pour la biologie synthétique

Synthetic biology is a science derived from the rapprochement between biotechnology and engineering science. It aims to create new biological systems through a rational combination between standardized biological elements which are disconnected from their natural context. Its main areas of application are the environment, the food-processing industry and the health sector. This thesis focuses on the ex vivo design aspects of these artificial biosystems. Thanks to analogies between biological processes and some electronic functions, the emphasis was put on reusing and adapting digital design tools that are fitting the top-down design approach. Thus, microelectronics CAD methods have been completely adapted to synthetic biology. In this regard, basic biological mechanisms have been modelled with various levels of abstraction, from digital abstraction to signal flow and conservative models. Fuzzy logic models have also been developed as a link between these levels of abstraction. These models have been implemented with two hardware description languages. They have been proven correct thanks to experimental results from state-of-the-art artificial biosystems. Concurrently to their formalization, improvements of design flow models have been studied: the modelling of interactions between several molecules have been made more realistic and the development of models for biological noise have been integrated to the process. This thesis is an important contribution to the structuring and the automation of some design steps for synthetic biosystems. It has made possible to highlight and to trace the outlines of a complete design flow, adapted from microelectronics.La biologie synthétique est une science issue du rapprochement entre les biotechnologies et les sciences pour l’ingénieur. Elle consiste à créer de nouveaux systèmes biologiques par une combinaison rationnelle d’éléments biologiques standardisés, découplés de leur contexte naturel. L’environnement, l’agroalimentaire et la santé figurent parmi ses principaux domaines d’application. Cette thèse s’est focalisée sur les aspects liés à la conception ex-vivo de ces biosystèmes artificiels. A partir des analogies réalisées entre les processus biologiques et certaines fonctions électroniques, l’accent a été mis sur la réutilisation et l’adaptation des outils de conception numériques, supportant l’approche de conception « top-down ». Ainsi, une adaptation complète des méthodes de CAO de la microélectronique a été mise en place pour la biologie synthétique. Dans cette optique, les mécanismes biologiques élémentaires ont été modélisés sous plusieurs niveaux d’abstraction, allant de l’abstraction numérique à des modèles flux de signal et des modèles conservatifs. Des modèles en logique floue ont aussi été développés pour faire le lien entre ces niveaux d’abstraction. Ces différents modèles ont été implémentés avec deux langages de description matérielle et ont été validés sur la base de résultats expérimentaux de biosystèmes artificiels parmi les plus avancés. Parallèlement au travail de formalisation des modèles destinés au flot de conception, leur amélioration a aussi été étudiée : la modélisation des interactions entre plusieurs molécules a été rendue plus réaliste et le développement de modèles de bruits biologiques a également été intégré au processus. Cette thèse constitue donc une contribution importante dans la structuration et l’automatisation d’étapes de conception pour les biosystèmes synthétiques. Elle a permis de tracer les contours d’un flot de conception complet, adapté de la microélectronique, et d’en mettre en évidence les intérêts

Structuring the design flow for synthetic biology

La biologie synthétique est une science issue du rapprochement entre les biotechnologies et les sciences pour l’ingénieur. Elle consiste à créer de nouveaux systèmes biologiques par une combinaison rationnelle d’éléments biologiques standardisés, découplés de leur contexte naturel. L’environnement, l’agroalimentaire et la santé figurent parmi ses principaux domaines d’application. Cette thèse s’est focalisée sur les aspects liés à la conception ex-vivo de ces biosystèmes artificiels. A partir des analogies réalisées entre les processus biologiques et certaines fonctions électroniques, l’accent a été mis sur la réutilisation et l’adaptation des outils de conception numériques, supportant l’approche de conception « top-down ». Ainsi, une adaptation complète des méthodes de CAO de la microélectronique a été mise en place pour la biologie synthétique. Dans cette optique, les mécanismes biologiques élémentaires ont été modélisés sous plusieurs niveaux d’abstraction, allant de l’abstraction numérique à des modèles flux de signal et des modèles conservatifs. Des modèles en logique floue ont aussi été développés pour faire le lien entre ces niveaux d’abstraction. Ces différents modèles ont été implémentés avec deux langages de description matérielle et ont été validés sur la base de résultats expérimentaux de biosystèmes artificiels parmi les plus avancés. Parallèlement au travail de formalisation des modèles destinés au flot de conception, leur amélioration a aussi été étudiée : la modélisation des interactions entre plusieurs molécules a été rendue plus réaliste et le développement de modèles de bruits biologiques a également été intégré au processus. Cette thèse constitue donc une contribution importante dans la structuration et l’automatisation d’étapes de conception pour les biosystèmes synthétiques. Elle a permis de tracer les contours d’un flot de conception complet, adapté de la microélectronique, et d’en mettre en évidence les intérêts.Synthetic biology is a science derived from the rapprochement between biotechnology and engineering science. It aims to create new biological systems through a rational combination between standardized biological elements which are disconnected from their natural context. Its main areas of application are the environment, the food-processing industry and the health sector. This thesis focuses on the ex vivo design aspects of these artificial biosystems. Thanks to analogies between biological processes and some electronic functions, the emphasis was put on reusing and adapting digital design tools that are fitting the top-down design approach. Thus, microelectronics CAD methods have been completely adapted to synthetic biology. In this regard, basic biological mechanisms have been modelled with various levels of abstraction, from digital abstraction to signal flow and conservative models. Fuzzy logic models have also been developed as a link between these levels of abstraction. These models have been implemented with two hardware description languages. They have been proven correct thanks to experimental results from state-of-the-art artificial biosystems. Concurrently to their formalization, improvements of design flow models have been studied: the modelling of interactions between several molecules have been made more realistic and the development of models for biological noise have been integrated to the process. This thesis is an important contribution to the structuring and the automation of some design steps for synthetic biosystems. It has made possible to highlight and to trace the outlines of a complete design flow, adapted from microelectronics