Comparative And Functional Genomics Databases

Ensembl Genome Browser. URL: http://www.ensembl.org/. Software system that produces and maintains automatic annotation on eukaryotic genomes (1).

Genome Bioinformatics Site. University of California, Santa Cruz (UCSC). URL: http://genome.ucsc.edu/. Contains the reference sequence and working draft assemblies for a large collection of genomes. Provides a portal to the Encyclopedia of DNA Elements (ENCODE) project.

BioCyc. URL: http://biocyc.org/. Pathway/genome databases of single organisms; MetaCyc has literature derived metabolic pathway data from many organisms.

Consortium for the Functional Genomics of Microbial Euk-aryotes. University of Manchester, U.K. URL: http://www. cogeme.man.ac.uk. Analysis of the transcriptome and proteome of Saccharomyces cerevisiae (yeast) and a number of plant and human fungal pathogens together with a bioinformatics centre.

Entrez Gene, NCBI, URL: http://www.ncbi.nih.gov/entrez. query.fcgi?db=gene. A searchable database of genes.

Gene OntologyTM (GO). URL: http://www.ncbi.nih.gov/entrez/ query.fcgi?db=gene. A searchable database of genes. The goal of GO is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. Provides three structured networks of defined terms to describe gene product attributes.

HOMOLOGENE. National Center for Biotechnology Information (NCBI). URL: http://www.ncbi.nlm.nih.gov/HomoloGene/. A system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.

Open Biological Ontologies (OBO). URL: http://obo.source-forge.net/. An umbrella Web address for well-structured vocabularies for shared use across different biological domains.

Reactome. Cold Spring Harbor Laboratory, European Bioin-formatics Institute and Gene Ontology Consortium. URL: http://www.reactome.org/. Curated database of biological processes in humans. It covers biological pathways ranging from the basic processes of metabolism to high-level processes such as hormonal signaling. While Reactome is targeted at human pathways, it also includes many individual biochemical reactions from nonhuman systems such as rat, mouse, fugu fish, and zebra fish.

RefSeq. NCBI. URL: http://www.ncbi.nlm.nih.gov/RefSeq/. A comprehensive, integrated, nonredundant set of reference sequences including genomic DNA, transcript RNA, and protein products, for major research organisms.

UniGene. NCBI. URL: http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?db=unigene. An experimental system for automatically partitioning GenBank sequences into a nonredundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.

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