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PMID: 20952411 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 39 ·No. Database issue ·2011-01-00 ·Pages D632-6

Arnaiz O, Sperling L

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.

MeSH Terms
Databases, Genetic Genome, Protozoan Genomics Paramecium tetraurelia/genetics Proteomics Software
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Arnaiz Olivier
Centre de Génétique Moléculaire, CNRS FRE3144, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
Sperling Linda
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkq918
Published
2011-01-00
Epub
2010-00-14
Pages
D632-6
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3013783
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkq918 PMC Full Text View journal details
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