Lepido-DB, a new bioinformatic resource for the annotation and cross-comparisons of lepidopteran genomes.
2009
Legeai, Fabrice | d'Alençon, Emmanuelle | Cousserans, François | Sezutsu, Hideki | Permal, Emmanuelle | Gordon, Karl | Quesneville, Hadi | Feyereisen, René | Fournier, Philippe | Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P) ; Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST | Biological systems and models, bioinformatics and sequences (SYMBIOSE) ; Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA) ; Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes) ; Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes) ; Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Centre Inria de l'Université de Rennes ; Institut National de Recherche en Informatique et en Automatique (Inria) | Biologie Intégrative et Virologie des Insectes [Univ. de Montpellier II] (BIVI) ; Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2) | National Institute of Agrobiological Sciences (NIAS) ; National Institute of Agrobiological Sciences | Unité de Recherche Génomique Info (URGI) ; Institut National de la Recherche Agronomique (INRA) | CSIRO Entomology [Canberra] ; CSIRO Entomology ; Commonwealth Scientific and Industrial Research Organisation [Australia] (CSIRO)-Commonwealth Scientific and Industrial Research Organisation [Australia] (CSIRO) | Institut Jacques Monod (IJM (UMR_7592)) ; Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS) | Institut Sophia Agrobiotech (ISA) ; Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)-Centre National de la Recherche Scientifique (CNRS)
International audience
Show more [+] Less [-]English. Lepido-DB is a centralized bioinformatic resource that was first developed to facilitate the comparative genomics of two major lepidopteran pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, by the analyzis of syntenic relationships and genome rearrangements of 15 pairs of BACs sequences and their corresponding colinear regions extracted from 10 Bombyx mori chromosomes. In this context, Lepido-DB Information System was designed to store, organize, display and distribute various genomic data and annotations of the three species. For instance, we supplied Lepido-DB with the KAIKOGAAS automatic annotations, the comparisons to insects proteomes and UniProt, the alignments of transcript sequences (retrieved from the Spodoptera SpodoBase, from CSIRO Helicoverpa ESTs or from NCBI Bombyx ESTs), the REPET pipeline's transposable elements predictions, or results of different cross-comparisons process to emphasize conserved regions and orthologous genes. The system was constructed using open source software tools from the Generic Model Organism Database (GMOD, http://www.gmod.org) including - a Chado database, - Gbrowse, a simple but rapid genome browser, - CMAP a graphical tool which facilitates the navigation within multiple maps or genome sequences, - Apollo, an application for the manual curation. Finally, beside a blast search and a full text search facilities, we released a gene report system offering gene information at a glance, such as transcripts and peptides sequences, functional annotations, or expression level based on its EST coverage. Lepido-DB can be accessed at http://www.inra.fr/lepidodb. In a larger scope, ensuing the AphidBase experience, this system may definitely support complete genomes sequencing and annotation projects, or any other project based on deep sequencing strategies (expression profiling by RNA-Seq, variability studies, ChIP- Seq, ...) for various Lep species.
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