euGenes: a eukaryote genome information system

euGenes is a genome information system and database that provides a common summary of eukaryote genes and genomes, at http://iubio.bio.indiana.edu/eugenes/. Seven popular genomes are included: human, mouse, fruitfly, Caenorhabditis elegans worm, Saccharomyces yeast, Arabidopsis mustard weed and zebrafish, with more planned. This information, automatically extracted and updated from several source databases, offers features not readily available through other genome databases to bioscientists looking for gene relationships across organisms. The database describes 150 000 known, predicted and orphan genes, using consistent gene names along with their homologies and associations with a standard vocabulary of molecular functions, cell locations and biological processes. Usable whole-genome maps including features, chromosome locations and molecular data integration are available, as are options to retrieve sequences from these genomes. Search and retrieval methods for these data are easy to use and efficient, allowing one to ask combined questions of sequence features, protein functions and other gene attributes, and fetch results in reports, computable tabular outputs or bulk database forms. These summarized data are useful for integration in other projects, such as gene expression databases. euGenes provides an extensible, flexible genome information system for many organisms.

[1]  S. Salzberg,et al.  Sequence and analysis of the Arabidopsis genome. , 2001, Current opinion in plant biology.

[2]  Wen Huang,et al.  The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant , 2001, Nucleic Acids Res..

[3]  Donna R. Maglott,et al.  RefSeq and LocusLink: NCBI gene-centered resources , 2001, Nucleic Acids Res..

[4]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[5]  Paul W. Sternberg,et al.  WormBase: network access to the genome and biology of Caenorhabditis elegans , 2001, Nucleic Acids Res..

[6]  David Botstein,et al.  SGD: Saccharomyces Genome Database , 1998, Nucleic Acids Res..

[7]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[8]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): integration nexus for the laboratory mouse , 2001, Nucleic Acids Res..

[9]  Thure Etzold,et al.  SRS - an indexing and retrieval tool for flat file data libraries , 1993, Comput. Appl. Biosci..

[10]  Jaime Prilusky,et al.  GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support , 1998, Bioinform..

[11]  Sarah A. Douglas,et al.  The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research , 2001, Nucleic Acids Res..

[12]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[13]  The FlyBase database of the Drosophila genome projects and community literature. , 2003, Nucleic acids research.