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GOBASE


NAR Molecular Biology Database Collection entry number 74
O'Brien, E.A., Zhang, Y., Wang, E., Yang, L., Marie, V., Lang, B.F., and Burger, G.
Center Robert-Cedergren for Bioinformatics and Genomics, Departement de Biochimie, Pavillon Roger-Gaudry, Universite de Montreal, 2900 Edouard-Montpetit, Montreal QC, H3T 1J4, Canada

Database Description

The organelle genome database GOBASE is now on its thirteenth release [September 2005] and contains 410,000 mitochondrial sequences including ~2500 complete genomes, and 128,000 chloroplast sequences including 43 complete genomes. Most of these are derived from GenBank entries, with some few being locally generated. GOBASE organises and integrates diverse data related to organelles, including nucleotide and protein sequences, taxonomic data, RNA secondary structures, and genetic maps, all of which are collected and verified by expert curators. The GOBASE interface includes search pages for sequences, genes, introns, exons, proteins, genetic maps and taxonomic data

Recent Developments

GOBASE has recently started including genome sequences of bacteria related to the ancestors of organelles; three genomes are currently included, of which one, that of Rickettsia prowazekii, has been fully reannotated, and the other two will be before the end of the year. Gene Ontology terms have been incorporated in the database. Deduced features based on incomplete annotations in GenBank have been added to the database. In cases where single genes in species are oversampled within GenBank, representative type examples are determined and only these examples are shown in the default interface configuration. Graphics illustrating the gene structure have been added for any gene more complicated than a single exon, and graphics representing the position of neighbouring genes have been added for all genes.

Acknowledgements

Support for GOBASE has been provided by operating grants from the Canadian Institutes of Health Research (CIHR), the Medical Research Council of Canada (MRC), and the Canadian Genome Analysis and Technology Program (CGAT), the Canadian Institute for Advanced Research (CIAR), Program in Evolutionary Biology, and by generous equipment grants from Sun Microsystems.


Go to the abstract in the NAR 2009 Database Issue.
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