MicroScope: a platform for microbial genome annotation and comparative genomics
David Vallenet,Stefan Engelen,Damien Mornico,Stéphane Cruveiller,Ludovic Fleury,Aurélie Lajus,Zoé Rouy,David Roche,Gregory Salvignol,Claude Scarpelli,Claudine Médigue +10 more
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TLDR
This article emphasizes the essential role of expert annotation as a complement of automatic annotation in microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone.Abstract:
The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http:// www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope’s rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone. Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcycread more
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Pathogenomics of the Ralstonia solanacearum Species Complex
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Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity
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TL;DR: This study integrated human epidemiological and clinical data with bacterial population genomics to harness the biodiversity of the model foodborne pathogen Listeria monocytogenes and decipher the basis of its neural and placental tropisms.
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MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
David Vallenet,Eugeni Belda,Alexandra Calteau,Stéphane Cruveiller,Stefan Engelen,Aurélie Lajus,François Le Fèvre,Cyrille Longin,Damien Mornico,David Roche,Zoé Rouy,Gregory Salvignol,Claude Scarpelli,Adam Alexander T. Smith,Marion Weiman,Claudine Médigue +15 more
TL;DR: Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly.
Journal ArticleDOI
PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data.
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TL;DR: A theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data is developed and validated using a set of phages with well-established packaging mechanisms representative of the termini diversity.
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Prophage WO genes recapitulate and enhance Wolbachia -induced cytoplasmic incompatibility
Daniel P. LePage,Jason A. Metcalf,Sarah R. Bordenstein,Jungmin On,Jessamyn I. Perlmutter,J. Dylan Shropshire,Emily M. Layton,Lisa J. Funkhouser-Jones,John F. Beckmann,Seth R. Bordenstein +9 more
TL;DR: Comparison and transgenic approaches are used to demonstrate that two differentially transcribed, co-diverging genes in the eukaryotic association module of prophage WO from Wolbachia strain wMel recapitulate and enhance cytoplasmic incompatibility.
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