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Nucleic Acids Research 2006 34(Database Issue):D697-D699; doi:10.1093/nar/gkj098
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Nucleic Acids Research, 2006, Vol. 34, Database issue D697-D699
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

GOBASE—a database of organelle and bacterial genome information

Emmet A. O'Brien*, Yue Zhang, LiuSong Yang, Eric Wang, Veronique Marie, B. Franz Lang and Gertraud Burger

Center Robert-Cedergren for Bioinformatics and Genomics, Département de Biochimie Pavillon Roger-Gaudry, Université de Montréal 2900 Edouard-Montpetit, Montréal, QC, Canada H3T 1J4

*To whom correspondence should be addressed. Tel: +1 514 343 6111; Fax: +1 514 343 7936; Email: eobrien{at}bch.umontreal.ca

Received September 13, 2005. Revised October 16, 2005. Accepted October 16, 2005.

The organelle genome database GOBASE is now in its twelfth release, and includes 350 000 mitochondrial sequences and 118 000 chloroplast sequences, roughly a 3-fold expansion since previously documented. GOBASE also includes a fully reannotated genome sequence of Rickettsia prowazekii, one of the closest bacterial relatives of mitochondria, and will shortly expand to contain more data from bacteria from which organelles originated. All these sequences are now accessible through a single unified interface. Enhancements to the functionality of GOBASE include addition of pages for RNA structures and a page compiling data about the taxonomic distribution of organelle-encoded genes; incorporation of Gene Ontology terms; addition of features deduced from incomplete annotations to sequences in GenBank; marking of type examples in cases where single genes in single species are oversampled within GenBank; and addition of graphics illustrating gene structure and the position of neighbouring genes on a sequence. The database has been reimplemented in PostgreSQL to facilitate development and maintenance, and structural modifications have been made to speed up queries, particularly those related to taxonomy. The GOBASE database can be queried at http://gobase.bcm.umontreal.ca/ and inquiries should be directed to gobase{at}bch.umontreal.ca.


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