GOBASE: an organelle genome database

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@bch.umontreal.ca.

[1]  Hideaki Sugawara,et al.  DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams , 2000, Nucleic Acids Res..

[2]  Michael W. Gray,et al.  RNA editing in plant mitochondria , 1989, Nature.

[3]  Domenica D'Elia,et al.  MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status , 2000, Nucleic Acids Res..

[4]  Thomas Meitinger,et al.  MITOP, THE MITOCHONDRIAL PROTEOME DATABASE , 2000 .

[5]  Flavio Licciulli,et al.  Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences , 1999, Nucleic Acids Res..

[6]  Timothy G. Littlejohn,et al.  The Organelle Genome Database Project (GOBASE) , 1998, Nucleic Acids Res..

[7]  Evelyn Camon,et al.  The EMBL Nucleotide Sequence Database , 2000, Nucleic Acids Res..

[8]  B. Paquin,et al.  The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression , 1997, Current Genetics.

[9]  B. Lang,et al.  A Comparative Genomics Approach to the Evolution of Eukaryotes and their Mitochondria 1 , 1999, The Journal of eukaryotic microbiology.

[10]  Timothy G. Littlejohn,et al.  A Portable Search Engine and Browser for the Entrez DataBase , 1994, J. Comput. Biol..

[11]  P F Lemkin,et al.  A World Wide Web (WWW) server database engine for an organelle database, MitoDat , 1996, Electrophoresis.

[12]  Pierre Baldi,et al.  An enhanced MITOMAP with a global mtDNA mutational phylogeny , 2006, Nucleic Acids Res..

[13]  Nelli Shimko,et al.  GOBASE: the organelle genome database , 2001, Nucleic Acids Res..

[14]  J. Boore.  Animal mitochondrial genomes. , 1999, Nucleic acids research.

[15]  G. Igloi,et al.  Editing of a chloroplast mRNA by creation of an initiation codon , 1991, Nature.

[16]  Emmet A. O'Brien,et al.  GOBASE—a database of organelle and bacterial genome information , 2005, Nucleic Acids Res..

[17]  R. Benne,et al.  Major transcript of the frameshifted coxll gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA , 1986, Cell.

[18]  Databases in peril , 2005, Nature Cell Biology.

[19]  Gertraud Burger,et al.  AutoFACT: An Automatic Functional Annotation and Classification Tool , 2005, BMC Bioinformatics.

[20]  Shamkant B. Navathe,et al.  MITOMAP: an update on the status of the human mitochondrial genome database , 1997, Nucleic Acids Res..

[21]  B. Lang,et al.  Mitochondrial genomes: anything goes. , 2003, Trends in genetics : TIG.

[22]  Thomas Meitinger,et al.  MITOP, the mitochondrial proteome database: 2000 update , 2000, Nucleic Acids Res..

[23]  Emmet A. O'Brien,et al.  GOBASE - a database of mitochondrial and chloroplast information , 2003, Nucleic Acids Res..

[24]  Marcella Attimonelli,et al.  HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research , 2005, BMC Bioinformatics.

[25]  B F Lang,et al.  Mitochondrial genome evolution and the origin of eukaryotes. , 1999, Annual review of genetics.

[26]  Domenica D'Elia,et al.  MitBASE: a comprehensive and integrated mitochondrial DNA database , 1999, Nucleic Acids Res..

[27]  E. O. Bregman,et al.  The Present Status. , 1926 .