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Nucleic Acids Res. 2011 Jan;39(Database issue):D632-6. doi: 10.1093/nar/gkq918. Epub 2010 Oct 14.

ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia.

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1
Centre de Génétique Moléculaire, CNRS FRE3144, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.

Abstract

ParameciumDB is a community model organism database built with the GMOD toolkit to integrate the genome and biology of the ciliate Paramecium tetraurelia. Over the last four years, post-genomic data from proteome and transcriptome studies has been incorporated along with predicted orthologs in 33 species, annotations from the community and publications from the scientific literature. Available tools include BioMart for complex queries, GBrowse2 for genome browsing, the Apollo genome editor for expert curation of gene models, a Blast server, a motif finder, and a wiki for protocols, nomenclature guidelines and other documentation. In-house tools have been developed for ontology browsing and evaluation of off-target RNAi matches. Now ready for next-generation deep sequencing data and the genomes of other Paramecium species, this open-access resource is available at http://paramecium.cgm.cnrs-gif.fr.

PMID:
20952411
PMCID:
PMC3013783
DOI:
10.1093/nar/gkq918
[Indexed for MEDLINE]
Free PMC Article

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