Genomic Databases

Genomic databases vary greatly in form and content

For organisms of major interest to geneticists, there is a long history of conventionally published catalogues of genes or mutations. In the past few years, most of these have been made available in an electronic form and a variety of new databases have been developed. These databases vary greatly in the classes of data captured and how these data are stored.

• Genomes Server - this server gives access to a hundreds of complete genome sequences, including those from archaea, bacteria, eukaryota, organelles, phages, plasmids, viroids and viruses.
  
  
• Proteome Analysis - the Proteome Analysis database has been set up to provide comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms.
  
  
• Ensembl - this is a joint project between the EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes. Ensembl presents up-to-date sequence data and the best possible automatic annotation for metazoan genomes. Available now are human, mouse, rat, fugu, zebrafish, mosquito, Drosophila, C. elegans, and C. briggsae.
  
  
• Karyn's Genomes - contains general information about organisms whose genomes are completely sequenced. The main aim of the database is to provide a short and concise explanation as to why it is important to obtain these organisms genomic sequences.
  
  
• WormBase - this is a repository of mapping, sequencing and phenotypic information for C. elegans (and some other nematodes).
  
  
• FlyBase - the database for Drosophila melanogaster is one of the best-curated genetic databases.
  
  
• MGD - the 'Mouse Genome Database' is one of the most comprehensively curated genetic databases.
  
  
• RGD - the 'Rat Genome Database' curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease.
  
  
• SGD - the 'Saccharomyces Genome Database' is another major yeast database. The MIPS yeast database is an important resource for information on the yeast genome and its products.
  
  
• SPGP - the 'S. Pombe Genome Project' based at the Sanger Institute is the database for genetic data on the fungus Schizosaccharomyces pombe.
  
  
• AceDB - this is the database for genetic and molecular data concerning Caenorhabditis elegans. The database management system written for AceDB by R. Durbin and J. Thierry-Mieg has proved very popular and has been used in many other species-specific databases. AceDB is now the name of this database management system, resulting in some confusion relative to the C. elegans database. The entire database can be downloaded from the Sanger Institute.
  
  
• HIV-SD - the 'HIV Sequence Database' collects, curates and annotates HIV and SIV sequence data and provides various tools for analysing this data.