Nucleic Acids Research Advance Access originally published online on October 25, 2008
Nucleic Acids Research 2009 37(Database issue):D946-D950; doi:10.1093/nar/gkn819
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Nucleic Acids Research, 2009, Vol. 37, Database issue D946-D950
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
GOBASE: an organelle genome database
Robert-Cedergren Center for Bioinformatics and Genomics, Département de Biochimie, Pavillon Roger-Gaudry, Université de Montréal, 2900 Edouard-Montpetit, Montreal QC, Canada H3T 1J4
*To whom correspondence should be addressed. Tel: +1 514 343 6111; Fax: +1 514 343 2210; Email: eobrien{at}bch.umontreal.ca
Received September 11, 2008. Revised October 10, 2008. Accepted October 13, 2008.
The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (
913 000) and chloroplast-encoded sequences (250 000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing data, with substitutions, insertions and deletions displayed using multiple alignments; (ii) addition of medically relevant information, such as haplotypes, SNPs and associated disease states, to human mitochondrial sequence data; (iii) addition of fully reannotated genome sequences for Escherichia coli and Nostoc sp., for reference and comparison; and (iv) a number of interface enhancements, such as the availability of both genomic and gene-coding sequence downloads, and a more sophisticated literature reference search functionality with links to PubMed where available. Future projects include the transfer of GOBASE features to NCBI/GenBank, allowing long-term preservation of accumulated expert information. The GOBASE database can be found at http://gobase.bcm.umontreal.ca/. Queries about custom and large-scale data retrievals should be addressed to gobase{at}bch.umontreal.ca.