GOBASE--a database of organelle and bacterial genome information.

Published

Journal Article

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@bch.umontreal.ca.

Full Text

Duke Authors

Cited Authors

  • O'Brien, EA; Zhang, Y; Yang, L; Wang, E; Marie, V; Lang, BF; Burger, G

Published Date

  • January 1, 2006

Published In

Volume / Issue

  • 34 / Database issue

Start / End Page

  • D697 - D699

PubMed ID

  • 16381962

Pubmed Central ID

  • 16381962

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

Digital Object Identifier (DOI)

  • 10.1093/nar/gkj098

Language

  • eng

Conference Location

  • England